Methods for Multiplex Imaging Using Labeled Nucleic Acid Imaging Agents

ABSTRACT

The present application provides certain advantageous ways of conducting multiplexed imaging.

This application is a continuation of U.S. application Ser. No.16/794,686, filed Feb. 19, 2020, which is a continuation of U.S.application Ser. No. 15/836,322, filed Dec. 8, 2017, which claims thebenefit of U.S. Provisional Application No. 62/432,511, filed Dec. 9,2016, and U.S. Provisional Application No. 62/445,896, filed Jan. 13,2017, the contents of each of which are incorporated by reference hereinin their entirety for any purpose.

DESCRIPTION Field

This application relates generally to the field of detection andquantification of analytes (e.g., targets).

Background

Fluorescence microscopy is a powerful tool for exploring molecules in,for example, a biological system. However, the number of distinctspecies that can be distinguishably and simultaneously visualized (i.e.the multiplexing power) is limited by the spectral overlap between thefluorophores. Some multiplexed imaging methods are known, but may notadequately produce a strong enough signal or may require specific meansof switching between targets being imaged. Thus, there is a need for newand improved multiplexed imaging methods employing improvedamplification methods and additional means of switching between targetsbeing imaged.

SUMMARY

In accordance with the description, in some embodiments, a method totest a sample for the presence of one or more targets comprises:

-   -   (1) contacting a sample being tested for the presence of one or        more targets with one or more target-specific binding partners,        wherein each target-specific binding partner is linked to a        nucleic acid strand and wherein target-specific binding partners        of different specificity are linked to different nucleic acid        strands,    -   (2) optionally removing unbound target-specific binding        partners,    -   (3) contacting the sample with a nonlinear amplifier strand        having complementarity to a nucleic acid strand, wherein the        nucleic acid strand is either a docking strand or a primer        strand,    -   (4) optionally removing unbound nonlinear amplifier strands,    -   (5) in either one or two steps amplifying the docking strand        with rolling circle amplification and contacting the sample with        labeled imager strands having complementarity to the docking        strand or amplified strand,    -   (6) imaging the sample to detect bound labeled imager strands,    -   (7) removing the bound labeled imager strands, and    -   (8) optionally repeating steps (1)-(8), or any subset thereof.

In some embodiments, a method to test a sample for the presence of oneor more targets comprises:

-   -   (1) contacting the sample with one or more target-specific        binding partners, wherein each target-specific binding partner        is linked to a nucleic acid strand, directly or indirectly, and        wherein target-specific binding partners of different        specificity are linked to different nucleic acid strands,    -   (2) optionally removing unbound target-specific binding        partners,    -   (3) wherein the nucleic acid strand is a docking strand or a        primer strand and if the nucleic acid is        -   (a) a docking strand, optionally increasing the number of            docking strands associated with each target-specific binding            partner, or        -   (b) a primer strand, optionally associating more than one            docking strand with the primer strand,    -   (4) contacting the sample with labeled imager strands capable of        binding a docking strand, directly or indirectly,    -   (5) optionally removing unbound labeled imager strands,    -   (6) imaging the sample to detect bound labeled imager strands,        and    -   (7) optionally extinguishing signal from the bound labeled        imager strand;    -   (8) optionally repeating steps (1)-(7) or any subset thereof.

In some embodiment, a composition comprises: a sample bound to more thanone target-specific binding partners, each binding partner bound to anucleic acid strand and at least one docking strand stably bound to alabeled imager strand, directly or indirectly, wherein the nucleic acidstrand is a docking strand or a primer strand if the nucleic acid is

-   -   (a) a docking strand, increasing the number of docking strands        associated with each target-specific binding partner, or    -   (b) a primer strand, associating more than one docking strand        with the primer strand.

In some embodiments, a composition comprises

-   -   (1) a label,    -   (2) a first nucleic acid domain, a second nucleic acid domain,        and a third nucleic acid domain, wherein each nucleic acid        domain is from 1 to 9 nucleotides long,    -   (3) a first linking moiety linking the first nucleic acid domain        and the second nucleic acid domain and    -   (4) a second linking moiety linking the second nucleic acid        domain and the third nucleic acid domain, wherein both linking        moieties are independently chosen from (a) an abasic site with        an intact phosphodiester backbone, (b) a linker cleavable by a        nucleic acid glycosylase, (c) non-natural nucleotides, or (d)        restriction site or a nicking site.

Additional objects and advantages will be set forth in part in thedescription which follows, and in part will be obvious from thedescription, or may be learned by practice. The objects and advantageswill be realized and attained by means of the elements and combinationsparticularly pointed out in the appended claims.

It is to be understood that both the foregoing general description andthe following detailed description are exemplary and explanatory onlyand are not restrictive of the claims.

The accompanying drawings, which are incorporated in and constitute apart of this specification, illustrate one (several) embodiment(s) andtogether with the description, explain the principles described herein.

BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed incolor. Copies of this patent or patent application publication withcolor drawings will be provided by the Office upon request and paymentof the necessary fee.

FIGS. 1A-E show a scheme of attaching Docking Strands to the target viaa target-recognizing moiety. Specifically, FIG. 1A shows Attachment ofthe Docking Strand to the target-recognizing moiety without signalamplification.

FIG. 1B shows attachment of the Docking Strand to the target-recognizingmoiety with signal amplification using a branched structure, which canbe created using processes such as HCR. FIG. 1C shows attachment of theDocking Strand to the target-recognizing moiety with signalamplification using a linear structure, which can be created usingprocesses such as RCA. FIG. 1D shows modified hybridization chainreaction (HCR), where a docking site (domain b) is attached to one ofthe two hairpins of HCR, allowing introduction of multiple docking sitesto one target-recognizing moiety. FIG. 1E shows rolling circleamplification to introduce multiple docking site (domain c-d) to onetarget-recognizing moiety. The following reference numbers are used inthis figure. 101: Target. 102: Target-recognizing moiety. 103: DockingStrand. 120: Primer strand of the HCR reaction that is attached to thetarget-recognizing moiety. 121: one hairpin of HCR, which is attachedwith the docking site. 122: another hairpin of HCR. 123-126: Sequentialhairpin assembly reactions. 127: Primer that is attached to thetarget-recognizing moiety. 128: linear template that can be circularizedby ligation. 129: The ligation reaction. 130: Primer extension with DNApolymerase with strand-displacement activity. 131: multiple dockingsites.

FIG. 2 shows sequential amplification, polymerization, anddendrimerization for amplified and removable signal.

FIG. 3 shows simultaneous amplification, polymerization, anddendrimerization for amplified and removable signal.

FIGS. 4A-B illustrate (A) sequential imaging with sequentialamplification from HRP-like enzymes and (B) simultaneous imaging withsequential amplification from HRP-like enzymes.

FIGS. 5A-D show removal of Imager Strand using nucleic acid-degradingenzymes. FIG. 5A shows a general scheme. FIG. 5B shows embodiments wherethere is a single deoxyuridine (dU) nucleotide in the DockingStrand-recognizing portion of the Imager Strand. FIG. 5C showsembodiments where there are multiple dU nucleotides in the DockingStrand-recognizing portion of the Imager Strand. FIG. 5D showsembodiments where the dU nucleotide is placed within the linkage betweenthe Docking Strand-recognizing portion and the signal-generating moietyof the Imager Strand. 104: imager strand. 105: signal generating moietyof the imager strand. 106: linkage between the target-recognizing moietyand the docking strand. 107: optional linkage to additional dockingstrands. 120: primer strand of the hybridization chain reaction (HCR)that is attached. 201: dU as an example of a moiety that can be degradedenzymatically. 202: The enzymatic reaction to degrade dU. 203: Theprocess where the remnant of the degradation reaction spontaneousdissociates from the Docking Strand.

FIGS. 6A-F shows removal of Imager Strand using polymerase enzymes. FIG.6A shows a self-priming hairpin is placed at the 3′ end of the ImagerStrand; the Imager Strand is removed using a polymerase withstrand-displacement activity (e.g., phi29). FIG. 6B shows a self-priminghairpin is placed at the 3′ end of the Imager Strand which is linked tothe signal-generating moiety via nucleic acid hybridization; the ImagerStrand is removed using a polymerase with strand-displacement activity.FIG. 6C shows a self-priming hairpin is placed at the 3′ end of theDocking Strand; the Imager Strand is removed using a polymerase withstrand-displacement activity. FIG. 6D shows a self-priming hairpin isplaced at the 3′ end of the Imager Strand; the Imager Strand is removedusing a polymerase with 5′-to-3′ exonuclease activity (e.g., DNAPolymerase I).

FIG. 6E shows a self-priming hairpin is placed at the 3′ end of theDocking Strand; the Imager Strand is removed using a polymerase with5′-to-3′ exonuclease activity. FIG. 6F shows the self-priming hairpin isreplaced by a hybridized duplex with an extendable 3′ end. 301:Self-priming hairpin. 302: The reaction where the self-priming hairpinor the hybridized duplex with an extendable 3′ end is extended by theDNA polymerase with strand-displacement activity. 303: The shortoligonucleotide that brings the signal-generating moiety to the ImagerStrand via hybridization. 304: The reaction where the self-priminghairpin or the hybridized duplex with an extendable 3′ end is extendedby the DNA polymerase with 5′-to-3′ exonuclease activity. 305:hybridized duplex with an extendable 3′ end. 306: Linkage between thetarget-recognizing moiety and the Docking Strand, wherein the linkagecomprises covalent or non-covalent interactions.

FIGS. 7A-G provide images after amplification. FIG. 7A provides aschematic illustrating the process of switching between fluorescenceimaging and brightfield imaging with DNA exchange and HRP-basedamplification. FIG. 7B provides the resulting fluorescence image oftonsil tissue cytokeratin labeled with antibody-DNA conjugate andcorresponding fluorescently labeled imager strand. FIG. 7C providesresulting brightfield immunohistochemistry image of cytokeratin in thesame tonsil tissue following DNA exchange and HRP-based chromogenicamplification. FIGS. 7D and E show fluorescence signal obtained fromcell samples stained for vimentin and DAPI without amplification (D,left) and with rolling circle amplification (E, right). FIG. 7F providesresulting fluorescence image of tonsil tissue cytokeratin labeled withantibody-DNA conjugate and corresponding fluorescently labeled imagerstrand (F, left). FIG. 7G, right, shows fluorescence image from the sametissue section after HCR amplification of the docking strands, andhybridization of the corresponding fluorescently labeled imager strand.In FIGS. 7D and 7E, the images show a DAPI nuclear stain in blue andappears as a generally round or bean-shaped object typically located inthe center region of a cell. DAPI stains the DNA inside the nucleus ofthe cell, and was included in the images as proof that there are cellspresent in the field of view. The vimentin staining (red) in FIG. 7D islower without amplification and in FIG. 7E brighter and more intensewith amplification. The red vimentin staining shows filament-like orwispy staining mainly outside of the cell nucleus.

FIG. 8 shows the use of pre-formed nonlinear DNA strands that can behybridized to docking strands as a starting point for rolling circlepolymerization.

FIGS. 9A-F and 9H-K show a series of images obtained in the Cy5 channelduring an exchange imaging experiment to reinterrogate a target in asample. FIG. 9G shows the average signal intensity in the images ofFIGS. 9A-F.

FIGS. 10A-B shows schematics and results for proximity detection withstable binding. Like FIGS. 7D-7E, FIGS. 10A-B show DAPI (blue) stainingof the nucleus inside of cells. FIG. 10A also shows alpha-tubulinstaining (green) primarily outside of the nucleus of the cell.

FIGS. 11A-C shows cell staining in an experiment designed to evaluateoff-target cross reactivity. These figures also use DAPI staining of thenucleus inside of cells (blue). Alpha-tubulin staining (red) is stronglypresent in FIG. 11A, absent in FIG. 11B, and weakly present in FIG. 11C.

FIGS. 12A-D show that the signal from a target can be almost completelyextinguished either using USER or UDG.

FIGS. 13A-D show various embodiments of exchange imaging, some usingprimer and intermediate strands in addition to imager and dockingstrands. FIG. 13A shows DNA-Exchange imaging with the use of anintermediate strand (401) to link an imager strand and a docking strandbound to a target through a target-recognition moiety. FIG. 13Billustrates a primer strand (404) used to amplify the number of dockingstrands associated with a target-binding complex, where the resultingamplified product (403) is attached to multiple docking sites (103) andcan be imaged with an imager strand, directly or indirectly through anintermediate strand as shown. FIG. 13C shows amplification of the numberof docking strands associated with a target using a primer strand toinitiate a hybridization chain reaction and imaging with the addition ofan imager strand, bound to docking strand through an intermediatestrand. FIG. 13D shows amplification of the number of docking strandsassociated with a target using a primer strand as a template forligation and rolling circle amplification, followed by the addition ofan imager strand, bound to docking strands through intermediate strandsfor imaging.

FIGS. 14A-D show removal efficiency of imager strands using nucleicacid-degrading enzymes varies with sequence design. Imager strands weresynthesized with (FIGS. 14B and 14D) and without (FIGS. 14A and 14C) anabasic site. Fluorescence images of CD3 in tonsil tissues labeled withantibody-DNA conjugates are shown before (FIGS. 14A-B, shown at a30,000-intensity scale) and after (FIGS. 14C-D, shown at a2,000-intensity scale) removal of the corresponding fluorescentlylabeled imager strands.

FIGS. 15A-F show an embodiment of exchange imaging in which four targetsare imaged using four imager strands labeled with two differentfluorophores, two targets at a time, sequentially. Thus, FIGS. 15A-15Fshows a combination of spectral and sequential multiplexing.

The following reference numbers are used throughout the figures and theapplication:

TABLE 1 Figure Reference Numbers 101 target 102 target-recognizingmoiety 103 docking strand 104 imager strand 105 signal generating moietyof the imager strand 106 linkage between the target-recognizing moietyand the docking strand 107 optional linkage to additional dockingstrands 120 primer strand of the hybridization chain reaction (HCR) thatis attached to the target-recognizing moiety 121 one hairpin of HCR,which is attached with the docking site 122 another hairpin of HCR 123-sequential hairpin assembly reactions 126 127 primer that is attached tothe target-recognizing moiety 128 linear template that can becircularized by ligation 129 the ligation reaction 130 primer extensionwith DNA polymerase with strand- displacement activity 131 multipledocking sites 201 dU as an example of a moiety that can be degradedenzymatically 202 the enzymatic reaction to degrade dU 203 the processwhere the remnant of the degradation reaction spontaneous dissociatesfrom the docking strand 301 self-priming hairpin 302 the reaction wherethe self-priming hairpin or the hybridized duplex with an extendable 3′end is extended by the DNA polymerase with strand-displacement activity303 the short oligonucleotide that brings the signal-generating moietyto the Imager Strand via hybridization 304 the reaction where theself-priming hairpin or the hybridized duplex with an extendable 3′ endis extended by the DNA polymerase with 5′-to-3′ exonuclease activity 305hybridized duplex with an extendable 3′ end 306 linkage between thetarget-recognizing moiety and the docking strand, wherein the linkagecomprises covalent or non-covalent interactions 401 intermediate strand402 amplification reaction 403 amplification product and associateddocking strands 404 primer

DESCRIPTION OF THE EMBODIMENTS I. Methods of Testing a Sample for thePresence of One or More Targets

This application relates to improved methods and compositions fortesting for the presence of one or more targets with one or more targetspecific binding partners.

Exchange Imaging is a method to achieve high multiplexing capability sothat many targets can be imaged on the same sample. The central conceptof Exchange Imaging involves the following steps: (1) attachingdifferent decodable information-carrying molecules (called dockingstrands) to different target-specific binding partners (such as but notlimited to an antibody that recognizes a target), whereintarget-specific binding partners of different specificity (i.e., bindingdifferent targets) are linked to different docking strands andoptionally removing unbound target-specific binding partners (2) using aset of molecules (called imager strands), each specifically recognizinga docking strand and carrying an observable moiety, to label a subset ofdocking strands, and imaging the corresponding subset of targets, (3)extinguishing the signal from the bound labeled imager strand byremoving the set of imager strands used in step 2, removing theobservable moiety from the imager strand, or inactivating the observablemoieties on such imager strands, and (4) using another set of imagerstrands, each specifically recognizing a docking strand and carrying anobservable moiety, to label another subset of docking strands, andimaging the corresponding subset of targets, (5) optionally, steps 3 and4 can be repeated to visualize multiple subsets of targets. End userswill readily appreciate that not all steps should be repeated in allexperiments. For example, in the last round of imaging, there would beno need to extinguish the signal from the bound labeled imager strandbecause no further imaging strands would be applied.

One non-limiting example of Exchange Imaging is DNA ExchangeImmunofluorescence, where one uses antibodies as the target-recognizingmolecules to image target proteins or other biomolecules, uses DNAoligonucleotides as docking strands, and uses DNA oligonucleotides thatare complementary to the docking strands and labeled with at least oneobservable moiety (such as a fluorophore) as the imager strands. In step3, extinguishing the signal from the bound labeled imager strandincludes several embodiments. In some embodiments, one may remove theimager strand, remove the label from the imager strand, and/or theinactivate the label attached to the imager strand. These variousmethods may be employed by using high temperature, low ionic strengthbuffers, denaturant (including formamide, for example), DNA helicase,DNase, strand displacement, chemical cleavage, enzymatic cleavage,chemical bleaching, photo-bleaching, and/or photochemical bleaching. Bybound labeled imager strand, we aim to distinguish the labeled imagerstrand that has, at one point, bound to the docking strand from theexcess labeled imager strand that did not bind to a docking strand.During the process of extinguishing the signal, the so-called boundlabeled imager strand may remain bound to the docking strand or it maynot remain bound to the docking strand.

In some embodiments, imaging the sample to detect bound labeled imagerstrands detects the presence of bound labeled imager strands. In someembodiments, imaging the sample to detect bound labeled imager strandsdetects the presence, location, and/or number of bound labeled imagerstrands.

Various types of imaging may be used in conjunction with the methods.For example, the imaging may include any type of microscopy that has anobjective, illumination, and a sensor. In some embodiments, imaging isperformed using a light microscope, fluorescence microscope includingwidefield, confocal (line and point scanning, spinning disk), totalinternal reflection (TIR), stimulated emission depletion (STED),light-sheet illumination (including lattice light-sheet illumination),structured illumination (SIM), expansion microscopy, and electronmicroscopy.

A. Amplification Methods

In microscopy, signal amplification is desired in many situations suchas when the abundance of target is low, when the allowable exposure timeis short, and/or when the sensitivity of the imaging equipment is low.Signal amplification offers advantages in DNA exchangeimmunofluorescence. In traditional, single-plex immunofluorescence(where only one target is analyzed), one often uses unconjugated primaryantibody and fluorescent-labeled secondary antibody. Because thesecondary antibodies are often polyclonal, multiple molecules ofsecondary antibody can bind to one molecule of primary antibody,resulting in amplification of signal. In DNA ExchangeImmunofluorescence, however, in some embodiments, users directly labelthe DNA docking strand to the primary antibody, thus eliminating suchsignal-amplification step obtained by using a polyclonal secondaryantibody. As a result, in some cases, DNA exchange immunofluorescencemay have lower signal intensity relative to traditionalimmunofluorescence.

Thus, in one embodiment, amplification is used to improve the signalintensity in multiplexed DNA exchange immunofluorescence. Many methodsfor signal amplification in microscopy exist, but not all can be appliedto DNA exchange immunofluorescence. One of the most well-known methodsinvolves linking (covalently or non-covalently) the target-recognizingmolecule (e.g., antibody) to an enzyme that can convert a non-observablesubstrate into an observable product. Many enzymes such as horseradishperoxidase (HRP), alkaline phosphatase (AP), glucose oxidase (GO),β-galactosidase (β-gal) have been used for these purposes. And an arrayof chromogenic, fluorogenic and chemiluminescent substrates for theseenzymes have been developed, such as 3,3′-diaminobenzidine (DAB), nitroblue tetrazolium chloride (NBT), 5-bromo-4-chloro-3-indolyl phosphate(BCIP), and 5-bromo-4-chloro-3-indoyl-β-D-galactopyranoside (X-Gal).Another strategy to exploit such enzymes in signal amplification is tocreate covalent bonds between the target (or other molecules in vicinityto the target) and an observable reporter molecule. This strategy isexemplified by tyramide signal amplification (TSA) technology that iscommercialized by Thermo Fisher and Perkin Elmer, among others. However,none of these signal-amplification methods is compatible with exchangeimaging, as the observable reporter, enzyme/primer or the substrate isbrought to the vicinity of the target permanently or without a decodabledocking strand. DNA-based (i.e., decodable) signal amplification methodswhere the observable signal can, at least in principle, be removed havebeen reported (e.g., Zimak, et al., Chembiochem 13(18):2722-8 (2012)(PMID: 23165916)). However, such methods involve multiple rounds ofmanipulation and the signal gain is modest.

Another type of signal amplification involves linking (covalently ornon-covalently) the target-recognizing molecule to a primer molecule ofa polymerization or dendrimerization reaction. On example of suchpolymerization reactions is rolling circle amplification (RCA) where theprimer of the RCA is linked to the target-recognizing molecule and isconverted to a long repetitive single-stranded DNA. Fluorescentmolecules can be either directly incorporated into the RCA product viafluorescent-labeled nucleotides, or be bound to the RCA product as apart of a fluorescent-labeled oligonucleotide that is designed tohybridize to the RCA product. Other examples of such polymerization ordendrimerization reactions include branched DNA toehold-based stranddisplacement (Schweller et al. PMCID: PMC3517005), hybridization chainreaction (HCR) (Dirks et al., 2014, PMID: 15492210, 24712299) and asimilar DNA hairpin-based dendrimerization reaction (Yin et al., 2008,PMID 18202654), which here we call HDR. Common applications ofamplification methods such as RCA, HCR, and HDR do not include theoption for Exchange Imaging, but could be compatible as demonstrated bythe improvements described herein.

Herein we discuss embodiments covering signal amplification that iscompatible with exchange imaging. We describe a series of embodimentsthat make signal amplification compatible with exchange imaging. Theseembodiments can be divided into two classes based on whether theamplification product is decodable. For example, if the amplificationproduct contains a docking strand component (e.g. single-stranded DNA),many (e.g., >5) antibodies against different targets can be programmedto generate such product of distinct docking strand sequences that canlater be decoded by the ssDNA molecules of complementary sequence. Thus,such amplification product is considered decodable. In such cases,signal amplification for different targets can be carried outsimultaneously, followed by simultaneous and/or sequential imaging ofdifferent amplification products. Simultaneous amplification carried outfor different targets can be considered multiplexed amplification.

In contrast, when the amplification product is a fluorophore or labelthat is covalently attached or noncovalently deposited near the targetbut does not contain a docking strand that could interact with an imagerstrand, these amplification products are considered undecodable. Forexample, when the enzyme responsible for signal amplification is HRP,the product is a chemical chromophore that does not allow manyvariations that can be specifically bound by many molecules serving asimager strands. In such cases, signal amplification for differenttargets may be carried out sequentially, and the enzyme linked to atarget that has already been amplified may be removed from the sample.Simultaneous signal amplification of undecodable amplification productsis possible if orthogonal enzyme-substrate pairs can be used.

Therefore, in some embodiments a method comprises (1) contacting asample being tested for the presence of one or more targets with one ormore target-specific binding partners, wherein each target-specificbinding partner is linked to a nucleic acid strand, and whereintarget-specific binding partners of different specificity are linked todifferent nucleic acid strands, (2) optionally removing unboundtarget-specific binding partners, (3) wherein the nucleic acid strand isa docking strand or a primer strand and if the nucleic acid is (a) adocking strand, increasing the number of docking strands associated witheach target-specific binding partner or (b) a primer strand, associatingmore than one docking strand with the primer strand (in either (a) or(b), such as, for example, amplifying the number of docking strandsavailable), (4) contacting the sample with labeled imager strandscapable of binding a docking strand, directly or indirectly, (5)optionally removing unbound labeled imager strands, (6) imaging thesample to detect bound labeled imager strands, (7) optionally removingthe bound labeled imager strands from the docking strands, and (8)optionally repeating steps (1)-(6), or any subset thereof.

By docking strands associated each target specific binding partner, hereand throughout the application, Applicant does not intend to requireamplification to occur on every single docking strand, but thatamplification generally occurs on the docking strands associated withthe various target-specific binding partners, as desired by the user(including amplifying only some docking strands participating indetecting targets A and B, while not amplifying docking strandsparticipating in detecting target B.) Amplification may also beincomplete, such as amplification occurring on only some but not all ofthe copies of the docking strand participating in detecting a giventarget. Additionally, amplification may replicate the entire dockingstrand or it may replicate only a portion of the docking strandsufficient for binding an imager strand.

Additionally, in some embodiments, a method comprises (1) contacting asample being tested for the presence of one or more targets with one ormore target-specific binding partners, wherein each target-specificbinding partner is linked to a nucleic acid strand and whereintarget-specific binding partners of different specificity are linked todifferent nucleic acid strands, (2) optionally removing unboundtarget-specific binding partners, (3) contacting the sample with labeledimager strands capable of binding a docking strand, directly orindirectly, wherein the nucleic acid strand in (1) is either a primerstrand or a docking strand and if the nucleic acid strand is a primerstrand, it is linked to a docking strand (4) optionally removing unboundlabeled imager strands, (5) imaging the sample to detect bound labeledimager strands and determine if amplification (step (7)) is required,(6) optionally removing the bound labeled imager strands from thedocking strands, (7) optionally increasing the number of docking strandsassociated with each target-specific binding partner (such as, forexample, amplifying the number of docking strands available by multiplemeans, including, but not limited to self-assembly of docking strandcomplexes, other assembly methods, branched and circular dockingstrands, etc.), and (8) optionally repeating steps (1)-(7), or anysubset thereof.

1. Amplification

Decodable Amplification Products.

Decodable amplification products include those cases in which theamplified product is a docking strand. In one embodiment, the dockingstrand does not contain an observable label. In one embodiment, thedocking strand serves as a barcode for an observable label (or imagerstrand). It should be noted at the outset that the docking strands, ordocking sites, may be introduced to the target during asignal-amplification reaction (FIG. 1b-c ), so that multiple dockingstrands are attached to one target molecule. Without being limiting,there are at least two strategies of achieving this: (Strategy 1)creating multiple docking sites that are attached to a scaffold, whichis in turn attached to the target-recognizing moiety (FIG. 1b ), and(Strategy 2) creating multiple binding sites on one piece of longsingle-stranded DNA that is attached to the target-recognizing moiety(FIG. 1c ).

One may use RCA, HCR or HDR to generate a polymeric or dendrimericproduct from the primer molecule linked to the antibody. In someembodiments, the product may contain many (e.g., greater than 2, 5, 10,15, 20, 25, 50, 100, etc.) copies of single-stranded DNA domains thatcan serve as the docking strand and thus be recognized byoligonucleotides serving as the imager strand. Such DNA domains may belong enough (e.g. 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, or morenucleotides long, or be able to bind its complementary strand with Kd<1nM at imaging condition). For RCA, this is achieved regularly. For HCRand HDR, if necessary one can include, at the loop or tail of thesubstrate hairpin, DNA domains that do not participate in thestrand-displacement cascades but constitute part or the entirety of theimager strand-binding site.

In one embodiment, a modified version of hybridization chain reaction(HCR) is employed for signal amplification, in which two hairpins (105and 106 of FIG. 1d ) are assembled onto the primer strand (104 of FIG.1d ) in an alternating fashion. Either or both of the two hairpins cancarry a docking site (domain b on hairpin 105 of FIG. 1d ). Tens tohundreds of hairpin units can be assembled onto one primer strand,brining tens to hundreds of docking sites to the target-recognizingmoiety. Several pairs of hairpin sequences (without the docking site)have been demonstrated by the Pierce group to enable successful HCRreactions. Hairpin sequences with the docking sites can be designed withthe same principle, although care may be taken to ensure that thedocking site does not form unwanted secondary structure with the rest ofthe hairpin.

In another embodiment, signal amplification involves linking (covalentlyor non-covalently) the target-recognizing molecule to a primer moleculeof a polymerization or dendrimerization reaction. On example of suchpolymerization reactions is rolling circle amplification (RCA, FIG. 1e )where the primer of the RCA is linked to the target-recognizing moleculeand is converted to a long repetitive single-stranded DNA. Fluorescentmolecules can be either directly incorporated into the RCA product viafluorescent-labeled nucleotides, or be bound to the RCA product as apart of a fluorescent-labeled oligonucleotide that is designed tohybridize to the RCA product.

There are many ways to carry out RCA, one of which is to first ensurethat the oligonucleotide conjugated to the target-recognizing moiety(here we call ‘primer’, 111 of FIG. 1e ) has an extendable 3′ end. Thenone can introduce a linear template strand (112 of FIG. 1e ) that canhybridize to the primer in the circular fashion, in which the primerbrings the two ends of the template together so that the two ends can beligated. Next, a ligase (such as T4 DNA ligase or CircLigase™ ssLigase,for example) is used to ligate the two ends to form a circle. After theligation the primer is hybridized to the circular template. Next, a DNApolymerase with strand-displacement activity (e.g., phi29, Bst,Vent(exo⁻)) can extend the primer along the circular template multiplerounds to create a concatemeric repeat. Part of the entirety of therepeat unit (domains c-d, or 115 of FIG. 1e ) can serve as the dockingsites (or docking strands) for imager strands.

An alternative method of RCA involves the use of a nonlinear amplifieror template strand, wherein an oligonucleotide (such as a dockingstrand) conjugated to the target-recognizing moiety is hybridized to acircular DNA template (amplifier strand), followed by extension of thedocking strand by a DNA polymerase to create a concatemeric repeat ofthe reverse complement of the amplifier strand (i.e. an amplified strandor RCA product). The hybridization of the amplifier strand to theoligonucleotide conjugated target-recognizing moiety may occur before(preassembly or prehybridization) or after the oligonucleotideconjugated target-recognizing moiety contacts the sample.

Thus, in some embodiments, at least one oligonucleotide-conjugatedtarget-recognizing moiety is hybridized to a nonlinear amplifier strandbefore being introduced to the sample. When the user chooses topre-assemble an antibody-DNA conjugate with an amplifier, a method totest a sample for the presence of one or more targets comprises (1)contacting a sample being tested for the presence of one or more targetswith one or more target-specific binding partners, wherein eachtarget-specific binding partner is linked to a nucleic acid strand andwherein target-specific binding partners of different specificity arelinked to different nucleic acid strands, and wherein at least onenucleic acid strand is hybridized to a nonlinear amplifier strand (2)optionally removing unbound target-specific binding partners, (3)amplifying the docking strand with rolling circle amplification (i.e.,increasing the number of docking strands or introducing a plurality ofdocking strands) to produce a rolling circle amplification product (4)contacting the sample with labeled imager strands having complementarityto the docking strand or the rolling circle amplification product, (5)imaging the sample to detect bound labeled imager strands, (6)optionally removing the bound labeled imager strands, and (7) optionallyrepeating steps (1)-(7), or any subset thereof. In this process, therolling circle amplification product comprises a concatemeric repeat ofthe reverse complement of the amplifier strand.

In another embodiment, imager strands may be hybridized to the RCAproduct (e.g. the concatemeric repeat of the reverse complement of theamplifier strand that is linked to the target-recognizing moiety) duringthe RCA reaction. In some embodiments, therefore, amplification occursusing rolling circle amplification, while in the presence of labeledimager strands having complementarity to the amplified strand. Forexample, a sample may be contacted with an oligonucleotide conjugated toa target-recognizing moiety that is either prehybridized to an amplifierstrand or the amplifier strand may be hybridized in a later step. Then,all additional components for the RCA reaction may be added in one stepincluding proteins (e.g. DNA polymerases, optionally BSA), nucleotides,buffer solution, salts, and imager strands. In some embodiments, a usermay wish to prevent the imager strand from being amplified. This can beaccomplished by several means, including, but not limited to employing a3′-modified imager strand having a modification on the 3′ end. Forexample, the 3′ modification on the imager strand may include a label(such as a fluorophore), a modified base, a stop code or terminator, a3′-O-modification, a dideoxy-C, a dideoxy-G, a dideoxy-A, a dideoxy-T,an inverted nucleotide, any modification that eliminates the presence ofa 3′ hydroxyl group, or a single-stranded extension of the 3′ end thatis not complimentary to the amplifier strand.

In addition to HCR and RCA, other examples of such polymerization ordendrimerization reactions include DNA hairpin-based dendrimerizationreaction (HDR) (Yin et al., 2008, PMID 18202654), and toe-hold mediatedstrand displacement.

DNA strand displacement is a method for the isothermal and dynamicexchange of DNA complexes. Strand displacement can be designed andintentionally controlled based on an understanding of DNA hybridizationinteractions and thermodynamics, and can be facilitated by introducingengineered handles which are known as “toehold domains.” The ability tomodulate binding interactions and exchange hybridization partners givesrise to a series of potential signal amplification applications.

In another embodiment, an encodable tyramide-based signal amplificationproduct is described. This method comprises (1) contacting a samplebeing tested for the presence of one or more targets with one or moretarget-specific binding partners, wherein each target-specific bindingpartner is linked to a nucleic acid strand and wherein target-specificbinding partners of different specificity are linked to differentnucleic acid strands, (2) optionally removing unbound target-specificbinding partners, (3) contacting the sample with enzyme-labeled strandscapable of binding a docking strand, wherein the nucleic acid strand in(1) is either a primer strand or a docking strand and if the nucleicacid strand is a primer strand, it is linked to a docking strand (5)optionally removing unbound enzyme-labeled strands, (4) contacting thesample with tyramide-bound docking strands, (5) enzymatically convertingthe tyramide moiety into an activated state, wherein the activated stateresults in a covalent linkage of the tyramide-bound docking strand tothe enzyme-labeled target site, (6) optionally quenching the enzymaticreaction, (7) removing the enzyme-labeled strands, and (8) optionallyrepeating a subset of steps 3-8. In one embodiment, the enzyme-linkedstrand is an HRP-linked strand.

In another embodiment, a method comprises (1) contacting a sample beingtested for the presence of one or more targets with one target-specificbinding partner, wherein the target-specific binding partner is linkedto an enzyme (2) optionally removing unbound target-specific bindingpartners, (3) contacting the sample with tyramide-bound docking strands,(4) enzymatically converting the tyramide moiety into an activatedstate, wherein the activated state results in a covalent linkage of thetyramide-bound docking strand to the enzyme-labeled target site, (5)quenching the enzymatic reaction, and (6) optionally repeating a subsetof steps 1-8, wherein target-specific binding partners of differentspecificity are introduced. In one embodiment, the enzyme-linkedtarget-specific binding partners contain HRP.

As shown in FIG. 2, the amplification of multiple targets can be carriedout sequentially. Alternatively, the amplification of multiple targetscan be carried out simultaneously (FIG. 3). Imaging steps can be carriedout between rounds of amplification, or following all rounds ofamplification.

Undecodable Amplification Products.

Undecodable amplification products include those cases in which theamplified product is an observable label that does not have specificaffinity for an imager strand. In one embodiment, the undecodableamplification product could be a fluorophore, chromogenic stain, ornanoparticle.

In one embodiment, a method to produce undecodable amplificationproducts comprises: (1) contacting a sample being tested for thepresence of one or more targets with one or more target-specific bindingpartners, wherein each target-specific binding partner is linked to anucleic acid strand and wherein target-specific binding partners ofdifferent specificity are linked to different nucleic acid strands, (2)optionally removing unbound target-specific binding partners, (3)contacting the sample with enzyme-labeled strands capable of binding adocking strand, wherein the nucleic acid strand in (1) is either aprimer strand or a docking strand and if the nucleic acid strand is aprimer strand, it is linked to a docking strand, (5) optionally removingunbound enzyme-labeled strands, (4) contacting the sample with asubstrate for the enzyme, (5) allowing an enzymatic reaction to producean amplification product, (6) quenching the enzymatic reaction, (7)imaging the sample to detect the presence or absence of one or moretargets, (8) removing the amplification product, and (9) repeating asubset of steps 1-9. Examples of enzymes that could be used include HRP,AP, GO, β-gal. When the enzyme is linked to an imager strand, i.e. astrand capable of binding a docking strand), sequential amplificationand imaging can be carried performed (FIG. 4). FIG. 4a illustrates amethod for sequential amplification and sequential imaging. Here, amethod is employed to remove or inactivate the amplification productbetween each imaging round. Removing or inactivating the amplificationproduct can be done by carefully choosing the substrate. For example,one may use a chromogenic substrate of HRP that is soluble insample-friendly organic solution (e.g., 3-amino-9-ethylcarbazole, whichis alcohol-soluble, PMID 19365090). In this case, after staining ofdocking strand-conjugated antibodies (FIG. 4a , Step 1), introducing theimager strand-conjugated HRP for one target and the substrate (FIG. 4,Step 2), and imaging the sample, one can use alcohol (e.g., methanol) toremove the HRP product and remove the imager strand using any of themethod described herein or their combination. Next one can introduce theimager strand-conjugated HRP for another target and repeat the process.

One may also use the TSA amplification method where the fluorophore canbe readily bleached. For example, many cyanine fluorophores and Alexafluorophore can be readily bleached by hydrogen peroxide in acidic orbasic conditions (PMID: 26399630). Alternatively, one can synthesize aTSA dye that contains a cleavable bond between the tyramide and thefluorophore. In this case the fluorophore can be inactivated by cleavingthis bond and washing.

FIG. 4b illustrates a method for sequential amplification andsimultaneous imaging. In this case, after staining of dockingstrand-conjugated antibodies (FIG. 4b , Step 1), introducing the imagerstrand-conjugated enzyme for one target and the substrate (FIG. 4, Step2, using HRP and TSA for example) to generate amplified product, one canremove the imager strand-conjugated enzyme without removing theamplified product, and repeat multiple rounds of amplification formultiple targets prior to imaging the sample in a single imaging step.

One may also use RCA, HCR, and HDR to achieve signal amplificationwithout decoding the amplification product. For example, aftermultiplexed antibody staining, one can add reagent (circular template inthe case of RCA, and substrate hairpins in the case of HCR and HDR) thatonly supports the polymerization/dendrimerization of one subset oftarget and directly incorporation of fluorescent dyes in theamplification product (e.g., via fluorescent-labeled nucleotides in thecase of RCA, and via fluorophore-labeled hairpin substrate in the caseof HCR and HDR). After imaging of this subset of targets andinactivation of the dye by bleaching or cleavage as described above, onecan introduce the reagent that supports thepolymerization/dendrimerization of another subset of targets anddirectly incorporation of fluorescent dyes in the amplification product.This process can then be repeated.

Multiple types of signal amplification can even be used in combination.For example, Gusev et al reported combining rolling circle amplificationand HRP-based signal amplification (PMID: 11438455).

One may replace the fluorophore (that is brought to the target via DNAcomplexes or other amplification method), by other molecule or moietiesthat can be directly or indirectly observed. These molecules or moietiesinclude, but are not limited to, metal particles, plasmonic enhancers,and proteins.

2. Nonlinear Amplification

A nonlinear DNA template could be employed for signal amplification as acircular amplification strand. A circular oligo, with complementarity toa docking strand, can be generated separately from the amplificationmethod. For example, ex situ ligation could be performed on a templateDNA strand to form a circular strand of DNA. A circular strand could behybridized to a docking strand that is attached to a target-specificbinding partner before contacting the sample. Alternatively, thetarget-specific binding partner could first be used to stain the sample,and then subsequently the circular strand could be introduced to thesample to hybridize with the docking strand on the target-specificbinding partner. Following the formation of a complex wherein a circularstrand is attached to a docking strand that is linked to atarget-specific binding partner, rolling circle amplification (RCA)could be carried out. This method offers certain advantages as it can beused to circumvent issues with inefficient in situ ligation steps.

In some situations, an amplifier strand may be employed. For example, insome embodiments, a method comprises (1) contacting a sample beingtested for the presence of one or more targets with one or moretarget-specific binding partners, wherein each target-specific bindingpartner is linked to a nucleic acid strand and wherein target-specificbinding partners of different specificity are linked to differentnucleic acid strands, (2) optionally removing unbound target-specificbinding partners, (3) contacting the sample with a nonlinear amplifierstrand having complementarity to a nucleic acid strand, wherein thenucleic acid strand in (1) is either a primer strand or a docking strand(4) optionally removing unbound nonlinear amplifier strands, (5)amplifying the docking strand with rolling circle amplification (i.e.,increasing the number of docking strands or introducing a plurality ofdocking strands), (6) contacting the sample with labeled imager strandscapable of binding a docking strand, either directly or indirectly, (7)imaging the sample to detect bound labeled imager strands, (8) removingthe bound labeled imager strands, and (9) optionally repeating steps(1)-(8), or any subset thereof.

In some embodiments, a polymerase may be used for RCA. In someinstances, the labeled imager strands are linear strands. In someinstances, the nonlinear amplifier strands are circular strands. In someinstances, the nonlinear amplifier strands are branched strands. In someinstances, the nonlinear amplifier strand becomes circular afterligation.

In some embodiments, amplification products may comprise a geometricshape, such as a triangle, quadrilateral, pentagon, hexagon, and thelike.

B. Variations in Method Steps

There are various ways of approaching multiplexed imaging, includingoptions for amplifying the signal using amplification steps at differenttime points and repeated steps to allow for imaging of multiple targetsor reinterrogation of a single target. Methods may also optionallyinclude extinguishing the signaling image at various points in time.

1. Amplifying Signal Before Applying Imager Strands and OptionallyExtinguishing Signal from the Bound Labeled Imager Strand

In some embodiments, a method to test a sample for the presence of oneor more targets comprises (1) contacting the sample with one or moretarget-specific binding partners, wherein each target-specific bindingpartner is linked to a nucleic acid strand and wherein target-specificbinding partners of different specificity are linked to differentnucleic acid strands, (2) optionally removing unbound target-specificbinding partners, (3) wherein the nucleic acid strand is a dockingstrand or a primer strand and if the nucleic acid is (a) a dockingstrand, increasing the number of docking strands associated with eachtarget-specific binding partner or (b) a primer strand, associating morethan one docking strand with the primer strand, (4) contacting thesample with labeled imager strands capable of binding a docking strand,either directly or indirectly, (5) optionally removing unbound labeledimager strands, (6) imaging the sample to detect bound labeled imagerstrands, and (7) optionally extinguishing signal from the bound labeledimager strand. In some instances, after step (4) and after optionallyperforming step (5) the method further comprises increasing the numberof docking strands associated with each target-specific binding partner.In some embodiments, the method further comprises removing unboundlabeled imager strand after the increasing the number of dockingstrands. Thus, in some modes, amplifying the docking strand with rollingcircle amplification occurs separately from contacting the sample withlabeled imager strands having complementarity to the amplified strand.By amplified strand, we mean the product of amplification (sometimesalso called the amplification product or the RCA product if rollingcircle amplification is employed).

In some instances, the sample is mounted to an optically transparentsupport. In some embodiments, the increase in the number of dockingstrands associated with each target-specific binding partner is achievedusing an enzyme. For example, the enzyme approaches described in SectionI.A above may be employed.

1. Amplifying Signal in the Presence of Imager Strands and OptionallyExtinguishing Signal from the Bound Labeled Imager Strand

In some embodiments, a method to test a sample for the presence of oneor more targets comprises (1) contacting the sample with one or moretarget-specific binding partners, wherein each target-specific bindingpartner is linked to a nucleic acid strand and wherein target-specificbinding partners of different specificity are linked to differentnucleic acid strands, (2) optionally removing unbound target-specificbinding partners, (3) contacting the sample with labeled imager strandscapable of binding a docking strand, either directly or indirectly, (4)wherein the nucleic acid strand is a docking strand or a primer strandand if the nucleic acid is (a) a docking strand, increasing the numberof docking strands associated with each target-specific binding partneror (b) a primer strand, associating more than one docking strand withthe primer strand, wherein the amplification occurs in the presence ofthe imager strand (5) optionally removing unbound labeled imagerstrands, (6) imaging the sample to detect bound labeled imager strands,and (7) optionally extinguishing signal from the bound labeled imagerstrand. In some instances, after step (4) and after optionallyperforming step (5) the method further comprises increasing the numberof docking strands associated with each target-specific binding partner.In some embodiments, the method further comprises removing unboundlabeled imager strand after the increasing the number of dockingstrands.

In some instances, the sample is mounted to an optically transparentsupport. In some embodiments, the increase in the number of dockingstrands associated with each target-specific binding partner is achievedusing an enzyme. For example, the enzyme approaches described in SectionI.A above may be employed.

The imager strands may have complementarity to the docking strand. Theimager strand may be a circular imager strand for rolling circleamplification. The imager strand may be an imager strand thatcircularizes in the presence of the docking strand and ligase. In someembodiments, the imager strand may comprise at least 2, 3, 4, 5, 6, 7,8, 9, or 10 regions that are complementary to the docking strand.

2. A Method to Test a Sample Mounted to an Optically Transparent Support

In some embodiments, a method to test a sample mounted to an opticallytransparent support for the presence of one or more targets comprises(1) contacting the sample with one or more target-specific bindingpartners, wherein each target-specific binding partner is linked to anucleic acid strand and wherein target-specific binding partners ofdifferent specificity are linked to different nucleic acid strands, (2)optionally removing unbound target-specific binding partners, (3)wherein the nucleic acid strand is a docking strand or a primer strandand optionally if the nucleic acid is (a) a docking strand, increasingthe number of docking strands associated with each target-specificbinding partner or (b) a primer strand, associating more than onedocking strand with the primer strand (4) contacting the sample withlabeled imager strands capable of binding a docking strand, eitherdirectly or indirectly, wherein the labeled imager strands are providedin a liquid medium or buffer solution (5) optionally removing unboundlabeled imager strands, (6) optionally removing liquid to create aliquid-free sample, (7) affixing a second optically-transparent materialparallel to the first support, and (8) imaging the sample to detectbound labeled imager strands.

In some embodiments, the second optically-transparent material is glassor plastic. In some instances, the second optically-transparent materialis from about 5 microns to 5 mm, from 50 microns to 500 microns, or from500 microns to 5 mm from the first support. In some instances, theimaging is carried out with an upright microscope.

In some embodiments, optionally removing liquid to create a liquid-freesample comprises preparing the sample for storage, such as long-termstorage for at least 4 hours, 1 day, 3 days, 1 week, 2 weeks, or onemonth. In some embodiments, optionally removing liquid to create aliquid-free sample increases sample handling convenience because theuser does not need to keep the sample hydrated.

By optionally removing liquid to create a liquid-free sample, this meansremoving at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,99%, or 100% of the liquid in a sample (namely, the liquid previously inthe sample and associated with the other sample components, such as thesample itself, the docking strand, the imager strand, etc.). In someembodiments, the mounting medium comprises air. In other embodiments,the mounting media comprises a mounting media in a gel formulation. Insome embodiments, the mounting media comprises a formula that begins asa liquid but changes to a gel or solid as time elapses (such as ahardening material, glue, cement, or other optically transparent andsimilarly-functioning material).

In other embodiments, the liquid in the sample may be replaced by aliquid mounting media such as a saline-based buffered solution (such asPBS).

Mounting media may be used to hold a specimen in place, to prevent asample from drying out, to more closely match the refractive index ofthe objective you will use, to prevent photobleaching (when notdesired), and to preserve a sample for long-term storage. The choice ofmounting media depends on the sample type, the imaging strategy, whichobservable moiety is used, and the objectives of the user (whether theuser wishes to hydrate the sample or whether the user wishes to storethe sample).

In some embodiments, a method to test a fixed sample mounted to anoptically transparent support for the presence of one or more targetscomprises (1) contacting the sample with one or more target-specificbinding partners, wherein each target-specific binding partner is linkedto a nucleic acid strand and wherein target-specific binding partners ofdifferent specificity are linked to different nucleic acid strands, (2)optionally removing unbound target-specific binding partners, (3)wherein the nucleic acid strand is a docking strand or a primer strandand if the nucleic acid is (a) a docking strand, increasing the numberof docking strands associated with each target-specific binding partneror (b) a primer strand, associating more than one docking strand withthe primer strand, (4) contacting the sample with labeled imager strandscapable of binding a docking strand, either directly or indirectly, (5)optionally removing unbound labeled imager strands, (6) optionallyremoving liquid to create a liquid-free sample, (7) affixing a secondoptically-transparent material parallel to the first support, and (8)imaging the sample to detect bound labeled imager strands.

In the various multiple embodiments, the optically transparent supportand the second optically transparent material parallel to the firstsupport may comprise a flow cell. In the various multiple embodiments,by parallel, it includes geometrical arrangements that are perfectlyparallel, as well as those that deviate from parallel by up to 1°, 2°,3°, 4°, 5°, 6°, 7°, 8°, 9°, or 10°.

3. Sample Reinterrogation

In some embodiments, users may desire to reinterrogate a sample for thesame target multiple times. When reinterrogation is desired, themultiplex imaging is conducted by conducting another round of imagingwith the same imager stand. Thus, when a user desires to image differenttargets, the imager strand has a unique nucleotide sequence relative toall other labeled imager strands. When a user desires to image the sametarget multiple times, the repeated steps use an imager strand that doesnot have a unique nucleotide sequence relative to all other labeledimager strands, but instead has the same sequence as a previouslyemployed imager strand.

Thus, in some embodiments, a method comprises (1) contacting a samplebeing tested for the presence of one or more targets with one or moretarget-specific binding partners, wherein each target-specific bindingpartner is linked to a nucleic acid strand and wherein target-specificbinding partners of different specificity are linked to differentnucleic acid strands, (2) optionally removing unbound target-specificbinding partners, (3) wherein the nucleic acid strand is a dockingstrand or a primer strand and optionally if the nucleic acid is (a) adocking strand, increasing the number of docking strands associated witheach target-specific binding partner or (b) a primer strand, associatingmore than one docking strand with the primer strand, (4) contacting thesample with labeled imager strands capable of binding a docking strand,either directly or indirectly, (5) optionally removing unbound labeledimager strands, (6) imaging the sample to detect presence, location, andnumber of bound labeled imager strands, (7) extinguishing signal fromthe bound labeled imager strand, and (8) repeating steps (3)-(6) or(3)-(7), with a labeled imager strand optionally having a uniquenucleotide sequence relative to all other labeled imager strands.

4. Spectral and Sequential Multiplexing

Two main methods exist for creating multiplexing in exchange imaging:spectral multiplexing and sequential multiplexing. Spectral multiplexingrefers to the ability to use different labels (such as differentfluorophores) in a single round of imaging. Spectral multiplexing doesnot necessitate extinguishing the signal from the first label beforeviewing the second label. For example, in the case of fluorophores,different excitation wavelengths of light can be used to individuallyexcite different fluorophores. This does not require separate rounds ofimaging. Sequential multiplexing refers to the ability to use the samelabels (such as the same fluorophore) in multiple rounds of imaging byextinguishing the signal from the first round of imaging before thesecond round of imaging. Spectral multiplexing and sequentialmultiplexing can either be used alone or in conjugation with each other.Using more than one technique of multiplexing, however, cansignificantly increase the number of targets that a user can visualizeduring a particular experiment.

In some embodiments, multiple rounds of imaging are performed with atleast some of the same fluorophores. For example, in a first round ofimaging, target A can be imaged with label X, target B can be imagedwith label Y, and target C can be imaged with label Z. As a next step,the signals from these labels can be extinguished. Then, in a secondround of imaging, target D can be imaged with label X, target E can beimaged with label Y, and target F can be imaged with label Z. Item Insome embodiments, at least two targets are imaged using at least twolabels, the signal extinguished, and then at least one more target isimaged using at least one of the same labels, wherein the imaging stepsmay be performed in either order. This means that the order of stepscould be reversed so the first imaging step comprises imaging at leastone target, the signal extinguished, and the second imaging stepcomprises imaging at least two targets.

Combining both spectral multiplexing and sequential multiplexing canincrease the overall convenience of performing the imaging for the userand reduce disruption to the sample being imaged.

C. Stable Binding

In some embodiments, at least some of the complementary agents used inimaging are stably binding to each other and in other embodiments, allthe complementary agents used in imaging are stably binding to eachother. In some embodiments, the docking strand is stably bound to theimager strand. In some embodiments, the amplifier strand is stably boundto the docking strand. In some embodiments, the amplifier strand isstably bound to the imager strand.

In some embodiments, the intermediate strand is stably bound to thedocking strand. In some embodiments, the intermediate strand is stablybound the amplifier strand. In some embodiments, the intermediate strandis stably bound the imager strand. In some embodiments, the amplifierstrand is stably bound to the imager strand. In some embodiments, theprimer strand is stably bound to the docking strand.

In some embodiments, a composition comprises a sample bound to more thanone target-specific binding partners, each binding partner bound to adocking strand, and at least one docking strand stably bound to alabeled imager strand.

In some embodiments, the stable binding comprises at least thepercentage binding for the time recited in Table 2. For example, Table 2includes 90% binding for at least 30 minutes. This means that of theitems bound at t=0, 90% of the items stay bound for at least 30 minutes.This also means that an equilibrium is achieved that has at least 90% ofthe docking strand bound to imager strand, for example, at any one timeand no more than 10% unbound. The stable binding can include anunbinding of some molecules and a rebinding of other molecules toachieve a population binding percentage; it does not require that atleast 90% are permanently bound, it only requires that at any one timeat least 90% are bound. Stable binding also can include, wherein V is avariable amount of time corresponding to the length required for theuser's experiment and an x means that percentage bound for the length oftime qualifies as stable binding:

TABLE 2 Stable Binding time (T) bound (at least) minutes hours days V 510 20 30 40 50 60 3 8 24 48 7 Percentage 50 x x x x x x x x x x x x xbound at 60 x x x x x x x x x x x x x time T 65 x x x x x x x x x x x xx 70 x x x x x x x x x x x x x 75 x x x x x x x x x x x x x 80 x x x x xx x x x x x x x 85 x x x x x x x x x x x x x 90 x x x x x x x x x x x xx 91 x x x x x x x x x x x x x 92 x x x x x x x x x x x x x 93 x x x x xx x x x x x x x 94 x x x x x x x x x x x x x 95 x x x x x x x x x x x xx 96 x x x x x x x x x x x x x 97 x x x x x x x x x x x x x 98 x x x x xx x x x x x x x 99 x x x x x x x x x x x x x 100 x x x x x x x x x x x xx

For example, stably bound may include 70%, 80%, or 90% binding at fromabout 5 minutes to 7 days, 10 minutes to 60 minutes, 20 minutes to 3hours, 30 minutes to 24 hours, 3 hours to 24 hours, or 24 hours to 7days.

The values in Table 2 apply to all types of stable binding discussedabove. Such measurements may be taken at imaging conditions (in somesituations room temperature, neutral pH, and physiological bufferconditions), after non-reactive buffer wash(es), or after anon-enzymatic buffer wash(es).

In some embodiments, the docking strand, primer strand, or intermediatestrand engaging in stable binding comprises 30 nucleotides or less, suchas from about 8 to 30 nucleotides, from 10 to 25 nucleotides, or from 10to 20 nucleotides. In some embodiments, the imager strand engaging instable binding comprises 30 nucleotides or less, such as from about 8 to30 nucleotides, from 10 to 25 nucleotides, or from 10 to 20 nucleotides.In some embodiments, the amplifier strand is from about 30 to 60nucleotides, 20 to 80 nucleotides, 30 to 70 nucleotides, 30 to 60nucleotides or more than 60 nucleotides. The type of amplificationreaction can also impact the length of the amplifier strand desired,with longer lengths desired for hybridization chain reaction (HCR), forexample. The person of ordinary skill in the art will recognize that thecomposition of different bases in the docking strand, imager strand,and/or amplifier strand will impact the number of nucleotides desired ineach strand due to affinity differences. Temperature will also impactthe number of nucleotides desired.

1. Proximity Imaging with Stable Binding

In some embodiments, a user may employ proximity imaging with stablebinding. In some embodiments, a composition comprises: (a) at least onefirst binding partner-oligonucleotide conjugate comprising a bindingpartner linked to an oligonucleotide that comprises a half-dockingdomain, an optional stability domain, and optionally a spacer domain;(b) at least one second binding partner-oligonucleotide conjugatecomprising a binding partner linked to an oligonucleotide that comprisesa half-docking domain, an optional stability domain, and optionally aspacer domain; wherein the stability domains of (a) and (b) arecomplementary to each other, and wherein the half-docking domains of (a)and (b) can combine linearly to form a full docking domain; and (c) atleast one labeled imager strand or intermediate strand comprising a 5′domain, a 3′ domain, and a linker domain located between the 5′ domainand the 3′ domain, wherein the 5′ domain is complementary to thehalf-docking domain of (a) and the 3′ domain is complementary to thehalf-docking domain of (b), and wherein the labeled imager strand orintermediate strand capable of being stably bound to the full dockingdomain and if an intermediate strand is used also providing a labeledimager strand. Alternatively, an intermediate strand may be used and becomplementary to both the docking strand and the imager strand.Amplification may also be employed. The stability criteria set forth inTable 2 also apply in this context.

In some embodiments, a user may employ proximity imaging with stablebinding when employing a primer. In some embodiments, a compositioncomprises: (a) at least one first binding partner-oligonucleotideconjugate comprising a binding partner linked to an oligonucleotide thatcomprises a half-primer domain, an optional stability domain, andoptionally a spacer domain; (b) at least one second bindingpartner-oligonucleotide conjugate comprising a binding partner linked toan oligonucleotide that comprises a half-primer domain, an optionalstability domain, and optionally a spacer domain; wherein the stabilitydomains of (a) and (b) are complementary to each other, and wherein thehalf-primer domains of (a) and (b) can combine linearly to form a fullprimer domain; (c) at least one docking strand capable of being stablybound to the full primer domain; and (d) at least one labeled imagerstrand capable of being stably bound to the docking strand or anintermediate strand capable of being stably bound to the docking strandand a labeled imager strand capable of being stably bound to theintermediate strand. The docking strand capable of being stably bound tothe full primer domain includes complementary binding (noncovalent) andextending from the same nucleic acid strand (covalent binding). Inembodiments where the docking strand is noncovalently bound to the fullprimer domain and has a complementary nucleic acid sequence, the dockingstrand may comprise a 5′ domain, a 3′ domain, and a linker domainlocated between the 5′ domain and the 3′ domain, wherein the 5′ domainis complementary to the half-primer domain of (a) and the 3′ domain iscomplementary to the half-primer domain of (b). In embodiments where thedocking strand is covalently bound, it may be extended out from the fullprimer domain by nucleic acid synthesis. Additionally and alternatively,an intermediate strand may be used and be complementary to both thedocking strand and the imager strand. Amplification may also beemployed. The stability criteria set forth in Table 2 also apply in thiscontext.

D. Control Experiments and Background Subtraction

Control experiments and background subtraction may be employed tofurther improve the results of the methods of testing a sample for thepresence of one or more targets. Neither of these aspects are requiredfor useful experimentation; however, both improve the quality ofmultiplexing and can be used alone or in conjunction with each other.

1. Control Experiments

Control measurements may be added at multiple time points in amultiplexed process. In some embodiments, a method to test a fixedsample mounted to an optically transparent support for the presence ofone or more targets comprises (1) contacting the sample with one or moretarget-specific binding partners, wherein each target-specific bindingpartner is linked to a nucleic acid strand and wherein target-specificbinding partners of different specificity are linked to differentnucleic acid strands, (2) optionally removing unbound target-specificbinding partners, (3) wherein the nucleic acid strand is a dockingstrand or a primer strand and optionally if the nucleic acid is (a) adocking strand, increasing the number of docking strands associated witheach target-specific binding partner or (b) a primer strand, associatingmore than one docking strand with the primer strand, (4) contacting thesample with labeled imager strands capable of binding a docking strand,either directly or indirectly, such as through an intermediate strand,(5) optionally removing unbound labeled imager strands, (6) imaging thesample to detect bound labeled imager strands, (7) extinguishing signalfrom the bound labeled imager strand, (8) performing a control step bycontacting the sample with labeled imager strands having a nucleotidesequence that is not complementary to a docking strand or intermediatestrand (i.e., one actually present in the method, if used, not ahypothetical intermediate strand), (9) optionally removing unboundlabeled imager strands, (10) imaging the sample to detect bound labeledimager strands, and (11) optionally extinguishing signal from the boundlabeled imager strand.

In some embodiments, a method to test a fixed sample mounted to anoptically transparent support for the presence of one or more targetscomprises (1) contacting the sample with one or more target-specificbinding partners, wherein each target-specific binding partner is linkedto a nucleic acid strand and wherein target-specific binding partners ofdifferent specificity are linked to different nucleic acid strands, (2)optionally removing unbound target-specific binding partners, (3)wherein the nucleic acid strand is a docking strand or a primer strandand optionally if the nucleic acid is (a) a docking strand, increasingthe number of docking strands associated with each target-specificbinding partner or (b) a primer strand, associating more than onedocking strand with the primer strand, (4) performing a control step bycontacting the sample with labeled imager strands having a nucleotidesequence that is not complementary to a docking strand or intermediatestrand (i.e., one actually present in the method, if used, not ahypothetical intermediate strand), (5) optionally removing unboundlabeled imager strands, (6) imaging the sample to detect presence,location, and/or number of bound labeled imager strands, (7)extinguishing signal from the bound labeled imager strand, (8)contacting the sample with labeled imager strands capable of binding adocking strand, either directly or indirectly, such as through anintermediate strand (9) optionally removing unbound labeled imagerstrands, (10) imaging the sample to detect presence, location, and/ornumber of bound labeled imager strands, and (11) optionallyextinguishing signal from the bound labeled imager strand.

In either of the above two embodiments, in some instances, the methodfurther comprises repeating steps (4)-(11). In some embodiments, theuser would not repeat the control steps. In other embodiments, the userwould repeat the control steps to assess noncomplementary binding.

In some of these embodiments, the labeled imager strand complementary tothe docket strand used in the repeated steps optionally has a uniquenucleotide sequence relative to at least one other labeled imagerstrands.

In some embodiments, the control experiment is used to assesscrossbinding of noncomplementary strands to ensure in an exampleassessing targets A, B, and C (for example) that the imager strand(imager A) intended to bind to the docking strand (docking A) affixed tothe target-specific binding partner (anti-A) for target A does notinteract with the docking strand affixed to the target-specific bindingpartner for B (imager B) or to measure the degree of its interaction. Insuch embodiments, repeated processes may evaluate the interaction ofimager C with docking strand A, etc. In these embodiments, thecomplementary strand (imager A binding to docking A) would notnecessarily be repeated.

2. Background Subtraction

In any of the embodiments discussed throughout this application, themethod may employ background subtraction. In some embodiments, themethod comprises imaging the sample to detect and/or measure abackground signal and subtracting the background signal from the imageof the sample to detect bound labeled imager strands. Such backgroundsignals may include autofluorescence and/or residual fluorescenceassociated with incompletely extinguishing signal from the bound labeledimager strands. In some aspects, the background signal is measuredbefore the image of the sample to detect bound labeled imager strands.In other aspects, the background signal is measured after the image ofthe sample to detect bound labeled imager strands.

E. Methods of Extinguishing Signal from the Bound Labeled Imager Strand

Various methods can be used to extinguish a signal from a bound labeledimager strand and this may be desired so that the same type ofdetectable moiety (such as a fluorophore) may be used on multiple imagerstrands so that the experiment is not spectrally limited.

In other words, removing the set of imager strands or inactivating theobservable moieties on the imager strands allows forspectrally-unlimited multiplex imaging. Some prior methods of multipleximaging were limited by the number of colors of fluorophores or otherimaging agents available. Removing the imager strands, removing labelsfrom imager strands, or inactivating the observable moieties allows forreuse of the same colors of fluorophores in a single experiment. In someembodiments, ideally, as much of the signal should be removed to ensureas low backgrounds as possible for continued imaging. In someembodiments, 100% of the prior signal-generating moiety is removed ordestroyed, while in some embodiments at least about 90%, 91%, 92%, 93%,94%, 95%, 96%, 97%, 98%, or 99% of the prior signal-generating moiety isremoved or destroyed.

Thus, extinguishing the signal from the labeled imager strand includesany method for removing the imager strand from binding, directly orindirectly, to the docking strand, removing the label from the imagerstrand, or inactivating the label on the imager strand.

All methods for extinguishing the signal from imager strands may beapplied to docking strands as well. In some embodiments, extinguishingthe signal from the bound labeled imager strand involves disrupting thelink between docking strand (or primer strand) and target-recognitionmoiety. In some embodiments, the docking strand comprises aphotocleavable linker that can be cleaved photochemically (e.g. by UVexposure, visible light, infrared, near infrared, x-ray, microwave,radio waves, or gamma rays). In some embodiments, the docking strand (orprimer strand) itself contains a moiety that can be cleaved by anenzyme. Examples of such enzymatically cleavable moieties include butare not limited to ribonucleotides, which can be cleaved by a variety ofRNases; deoxyuridines, which can be cleaved by enzyme combinations suchas USER (New England Biolabs); and restriction sites, which can becleaved by sequence-specific nicking enzymes or restriction enzymes. Insome embodiments, the docking nucleic acid comprises a deoxyuridine, inwhich the uracil group may be cleaved by uracil-DNA glycosylase. In someembodiments, the docking nucleic acid comprises an abasic site, whichmay be cleaved by endonuclease.

One non-limiting example of Exchange Imaging is DNA ExchangeImmunofluorescence, where one uses antibodies as the target-recognizingmolecules to image target proteins or other biomolecules, uses DNAoligonucleotides as docking strands, and uses DNA oligonucleotides thatare complementary to the docking strands and labeled with fluorophoresas the imager strands. A user may extinguish the signal from the labeledimager strand by using high temperature, denaturant, DNA helicase,DNase, and/or strand displacement, or may remove the fluorophores on theimager strands by chemical cleavage, enzymatic cleavage, chemicalbleaching, photo-bleaching, and/or photochemical bleaching.

1. Nucleic Acid-Degrading Enzymes

A number of enzymes can break the covalent bonds within a nucleic acidmolecule. For example, some glycosylase can remove the base from thesugar moiety of a nucleotide, endonuclease can cut the bond within thephosphodiester bridge inside the nucleic acid molecule, whileexonuclease can similarly break the phosphodiester bridge at the 5′ or3′ terminal of the nucleic acid molecule in a sequential fashion.Another example comprises DNAzymes or deoxyribozymes, oligonucleotideswith catalytic activity capable of cleaving the phosphodiester bond innucleic acid molecules. All these types of enzymes may be engineered forimager strand removal (FIG. 5) and constitute enzymatically cleaving,modifying, or degrading the labeled imager strand nucleic acids.

Glycosylase.

If a glycosylase can specifically remove a base that participates thebase-pairing between the Docking Strand and the Imager Strand, it canreduce the strength of interaction between the two strands. For example,one can use deoxyuridine (dU) to replace deoxythymidine (dT) in theImager Strand. dU can pair with dA in the Docking Strand just like thedT does, but can be specifically removed by Uracil-DNA Glycosylase (UDG,commercially available from New England Biolabs, Cat #M0280S). Thisreaction will result in abasic site(s) on the Imager Strand. Such abasicsites can be further cleaved by Endonuclease VIII. This will furtherpromote the dissociation between the remnant of Imager Strand and theDocking Strand. Enzyme blend comprising both UDG and Endonuclease VIIIis also commercially available (e.g., from New England Biolabs, underthe tradename USER, Cat #M5505S). One may place from about 1 to 20, 1 to15, 1 to 10, or 1 to 5 dU nucleotides in the Imager Strand. With USER,the dUs may be placed in a way that after removal of U, the remnants areshort enough (e.g., less than or equal to about 9, 8, 7, 6, 5, 4, 3, 2,or 1 nucleotides) that they dissociate spontaneously and quickly. Ifonly UDG (i.e., no Endonuclease VIII) is used, the removal of dU unitscould destabilize the strand enough to facilitate removal. Total numberof base pairs between the imager strand and docking strand after dUremoval may be less than or equal to 9, 8, 7, 6, 5, 4, 3, 2, or 1nucleotides. Thus, in some embodiments the imager strand or intermediatestrand may comprise at least one U capable of cleavage by USER.

The sequence of the remnants, as well as the temperature, will impacthow short the remnants should be to dissociate spontaneously. Forexample, a sequence high in GC content might have more binding affinityat a shorter length than another sequence at a longer length. Thus, insome instances, a 9-mer may be sufficient for stable binding and inother instances a 9-mer may be sufficient to dissociate. A person ofordinary skill in the art can evaluate the sequences, temperatures, andaffinities, here and in the cleavage of non-natural nucleotidesdiscussed below.

Restriction endonuclease and nicking endonuclease.

One may engineer a restriction site in the docking strand:imager strandduplex. This allows the usage of the corresponding restrictionendonuclease to cut such restriction site, which breaks the linkagebetween the target and the signal-generating moiety of the imagerstrand. As an example, Cas9 (CRISPR associated protein 9) is aRNA-guided endonuclease that can be used to specifically cleave docking:imager strand duplexes, by engineering a specific recognition site inthe corresponding sequences. This results in both strands being cleaved,preventing one from re-interrogating the corresponding target. To solvethis problem, one can use nicking endonuclease which only cut onestrand. As an example, Cas9 nickases are Cas9 enzymes that have beenengineered to only include one active cleaving site, leading to singlestrand cuts, while conserving the high specificity of Cas9. One candesign the restriction site in a way that only the imager strand is cut,and that the remnant of imager strand that carries the signal-generatingmoiety is sufficiently short (e.g., <7 nucleotide) that it dissociatesspontaneously and quickly from the docking strand. Other examples ofendonucleases with site specific activity include but are not limitedto: zinc finger nucleases, transcription activator-like effectornucleases (TALENs), and deoxyribozymes.

Rnase.

One may make some or all of nucleotides in the imager strand RNAnucleotides (also called ribonucleotides), instead of DNA nucleotides(also called deoxynucleotide). Such RNA nucleotides can be removed byRnase. If the docking strand is comprised of DNA nucleotides and theimager strand contains RNA nucleotides, such RNA nucleotides in theDNA:RNA heteroduplex can be removed by Rnase H.

Polymerase.

The imager strand can also be removed by using polymerases withstrand-displacement activity or 5′-to-3′ exonuclease activity. Forexample, one can engineer a hairpin structure at the 3′ end of thedocking strand made of DNA. When a DNA polymerase with stranddisplacement activity (e.g., Phi29, Bst, Vent) is introduced andsupplied with suitable buffer and dNTPs, the 3′ of the docking strandcan be extended, during which the imager strand is displaced (FIG. 6c ).The self-priming hairpin can also be engineered on the imager strand(FIG. 6a-b ), for which the signal-general moiety can be either attachedto the imager strand directly (FIG. 6a ), or attached to the imagerstrand via DNA hybridization (FIG. 6b ). When a DNA polymerase with5′-to-3′ exonuclease activity (e.g., DNA polymerase I, Taq) isintroduced and supplied with suitable buffer and dNTPs, and aself-priming hairpin is engineered at the 3′ end of the docking strand,the 3′ can be extended, during which the imager strand is degraded (FIG.6e ) Similar effect can be achieved if the self-priming hairpin isengineered at the 3′ end of the imager strand (FIG. 6d ). Note that theself-priming hairpin can also be replaced by a stable duplex (e.g., FIG.6f ).

Cleavage of Non-Natural Nucleotides.

Non-natural nucleotide that serve as substrates for particular enzymesmay be used. For example, 8-oxoguanine may be cleaved by DNA glycosylaseOGG1. Abasic sites may also be incorporated into a DNA strand, such asan imager strand, which may be cleaved by an endonuclease. For example,a 1′,2′-Dideoxyribose, dSpacer, apurinic/apyrimidinic, tetrahydrofuran,or abasic furan may be cleaved by Endonuclease VIII. Thus, in someembodiments the imager strand or intermediate strand may comprise atleast one abasic site capable of cleavage by Endonuclease VIII. In someembodiments the imager strand or intermediate strand may comprise atleast one deoxyuridine and at least one abasic site capable of cleavageby USER, UDG, or Endonuclease VIII. Photocleavable spacers or RNA abasicsites may also be used, such as ribospacer (rSpacer) or Abasic IImodification. Other pairs of non-natural nucleotides and their pairedenzymes may be employed.

Thus in some embodiments, a composition comprises (1) a label, (2) afirst nucleic acid domain, a second nucleic acid domain, and a thirdnucleic acid domain, wherein each nucleic acid domain is from about 1 to9 nucleotides long (for example, about 9, 8, 7, 6, 5, 4, 3, 2, or 1nucleotides), (3) a first linking moiety linking the first nucleic aciddomain and the second nucleic acid domain and (4) a second linkingmoiety linking the second nucleic acid domain and the third nucleic aciddomain, wherein both linking moieties are independently chosen from (a)an abasic site with an intact phosphodiester backbone, (b) a linkercleavable by a nucleic acid glycosylase, or (c) a restriction site ornicking site. In some embodiments, additional nucleic acid domains arelinked by additional linking moieties. In some embodiments, at least onelinking moiety is an abasic site (apyrimidinic) with an intactphosphodiester backbone. In some embodiments, at least one linkingmoiety is susceptible to cleavage from Endonuclease VIII. In someembodiments, the nucleic acid domains comprise DNA and in some thenucleic acid domains comprise RNA. In some aspects, at least one linkingmoiety comprises at least one non-natural nucleotide. In some aspects,at least one linking moiety comprises 8-oxoguanine.

In some embodiments, methods of removing imager strand may be combinedwith amplification steps. In some embodiments, a method to test a samplefor the presence of one or more targets comprises (1) contacting thesample with one or more target-specific binding partners, wherein eachtarget-specific binding partner is linked to a nucleic acid strand,directly or indirectly and wherein target-specific binding partners ofdifferent specificity are linked to different nucleic acid strands, (2)optionally removing unbound target-specific binding partners, (3)wherein the nucleic acid strand is a docking strand or a primer strandand if the nucleic acid is (a) a docking strand, increasing the numberof docking strands associated with each target-specific binding partneror (b) a primer strand, associating more than one docking strand withthe primer strand, (4) contacting the sample with labeled imager strandscapable of binding a docking strand, directly or indirectly, wherein thelabeled imager strands comprise the composition described immediatelyabove, (5) optionally removing unbound labeled imager strands, (6)imaging the sample to detect bound labeled imager strands, (7) removingthe bound labeled imager strands from the docking strands, wherein thelabeled imager strands are removed from the docking strands byenzymatically cleaving, modifying, or degrading the labeled imagernucleic acids, and (8) optionally repeating steps (1)-(7), or any subsetthereof.

In some aspects, the labeled imager nucleic acids are removed byenzymatically cleaving the labeled imager strand.

F. Description of Samples

1. Types of Samples

Various types of samples may be imaged using these methods. In someembodiments, the sample is a fixed sample. In some embodiments, thesample is a cell, cell lysate, tissue, tissue lysate, and or a wholeorganism. In some embodiments, the sample is a cell or tissue sample, acell or tissue lysate, or a bodily fluid. In some embodiments, thesample is tissue and the imaging comprises in-tissue multiplexing forimmunostaining.

The sample may be provided in a liquid medium or buffer solution.

2. Antigen Retrieval

In some embodiments, staining a sample with a target-specific bindingpartner requires specific conditions and not all target-specific bindingpartners will bind to their antigens under the same conditions. This maybe because their target antigens are not available under the sameconditions.

Thus in some embodiments, a method to test a sample for the presence ofone or more targets comprises (1) treating the sample to expose one ormore previously unavailable targets, (2) contacting the sample with oneor more target-specific binding partners, wherein each target-specificbinding partner is linked to a nucleic acid strand, and whereintarget-specific binding partners of different specificity are linked todifferent nucleic acid strands, (3) optionally removing unboundtarget-specific binding partners, (4) wherein the nucleic acid strand isa docking strand or a primer strand and optionally if the nucleic acidis (a) a docking strand, increasing the number of docking strandsassociated with each target-specific binding partner or (b) a primerstrand, associating more than one docking strand with the primer strand,(5) contacting the sample with labeled imager strands capable of bindinga docking strand, directly or indirectly, (6) optionally removingunbound labeled imager strands, (7) imaging the sample to detect boundlabeled imager strands, (8) extinguishing signal from the bound labeledimager strand, and (9) optionally repeating steps (1)-(8), each time (a)exposing a different set of previously unavailable targets (b) using oneor more different target-specific binding partners and (c) using alabeled imager strand having a unique nucleotide sequence relative to atleast one other labeled imager strand.

3. Description of Targets and Use in Identifying Biomarkers

In some embodiments, the method is useful for identifying a biomarker.In some instances, samples are imaged and data analysis performed onthose samples. In some embodiments, multiple targets are tested forusing corresponding target-specific binding partners for each target. Insome instances, the relationship between different targets may beassessed; for example, a user might seek to determine the relationshipof multiple markers to a disease state and conclude that the diseasesample has increased levels of A, decreased levels of B, and levels of Cwithin a certain range, as compared to healthy tissue that does not havethat biomarker distribution.

In some embodiments, at least 10, 96, 100, 384, or 500 samples areimaged and data analysis performed on those samples.

In some embodiments, at least 5, 10, 15, 25, 30, 50, 75, or 100 or moretargets are tested for using corresponding target-specific bindingpartners for each target.

G. Equipment and Software

1. Imaging Chamber, Such as a Flow Cell

In some embodiments, an imaging chamber can be employed. In someinstances, an imaging chamber is a fixed chamber with no inlet and nooutlet. In some embodiments, an imaging chamber has a singleinlet/outlet combination. In other instances, an imaging chamber allowsfor flow and is designated a flow cell. A flow cell may be comprised ofa first optically transparent support in combination with a secondoptically transparent material (such as a glass or plastic coverslip) toprovide a flow cell with a top and bottom surface and fluid flow betweenthem. If a first and second optically transparent material are used,they may be placed parallel to each other. By parallel, it includesgeometrical arrangements that are perfectly parallel, as well as thosethat deviate from parallel by up to 1°, 2°, 3°, 4°, 5°, 6°, 7°, 8°, 9°,or 10°. In some embodiments, the second optically transparent materialis in close proximity to the first optically transparent material, suchas about 5 microns to 5 mm, from 50 microns to 500 microns, or from 500microns to 5 mm.

An imaging chamber may also be comprised of a first opticallytransparent support and a gasket (also referred to as an isolator orspacer). The gasket may be open to the air on the top surface or it maybe closed and have an optically transparent top surface. The gasket mayhave a combined inlet/outlet or it may have both an inlet and an outlet.The gasket may also have no outlet. The gasket may be plastic, rubber,adhesive. A gasket may comprise a CoverWell Chamber Gasket (ThermoFisher), an ultra-thin sealed chamber for upright and invertedmicroscopes (Bioscience Tools), or an incubation chamber (GraceBio-Labs, including HybriSlip™ hybridization covers, HybriWell™ sealingsystem, CoverWell™ incubation chambers, imaging spacers, SecureSeal™hybridization chambers, FlexWell™ incubation chambers, FastWells™reagent barriers, and Silicone Isolators™).

In some instances, a gasket may be employed along with a coverslipforming the top surface of an imaging chamber or flow cell.

Imaging chambers, such as but not limited to flow cells, may be reusableor disposable.

Thus, in some embodiments, a method to test a fixed sample mounted to afirst optically transparent support for the presence of one or moretargets comprises (1) contacting the sample with one or moretarget-specific binding partners, wherein each target-specific bindingpartner is linked to a nucleic acid strand and wherein target-specificbinding partners of different specificity are linked to differentnucleic acid strands, (2) optionally removing unbound target-specificbinding partners, (3) wherein the nucleic acid strand is a dockingstrand or a primer strand and optionally if the nucleic acid is (a) adocking strand, increasing the number of docking strands associated witheach target-specific binding partner or (b) a primer strand, associatingmore than one docking strand with the primer strand, (4) in an imagingchamber (such as a flow cell), contacting the sample with labeled imagerstrands capable of binding a docking strand, directly or indirectly, (5)optionally removing unbound labeled imager strands, (6) imaging thesample to detect presence, location, and/or number of bound labeledimager strands and optionally removing the imaging chamber, (7)extinguishing signal from the bound labeled imager strand, and (8)repeating steps (4)-(6) or (4)-(7), at least once with a labeled imagerstrand optionally having a unique nucleotide sequence relative to atleast one other labeled imager strands.

A method to image a fixed sample mounted to an optically transparentsupport comprising (1) contacting the sample with one or moretarget-specific binding partners, wherein each target-specific bindingpartner is linked to a nucleic acid strand, and wherein target-specificbinding partners of different specificity are linked to differentnucleic acid strands, (2) optionally removing unbound target-specificbinding partners, (3) wherein the nucleic acid strand is a dockingstrand or a primer strand and if the nucleic acid is (a) a dockingstrand, increasing the number of docking strands associated with eachtarget-specific binding partner or (b) a primer strand, associating morethan one docking strand with the primer strand, (4) contacting thesample with labeled imager strands capable of binding a docking strand,either directly or indirectly, (5) optionally removing unbound labeledimager strands, (6) optionally removing liquid to create a liquid-freesample, (7) affixing a second optically-transparent material in closeproximity to (namely about 5 microns to 5 mm, from 50 microns to 500microns, or from 500 microns to 5 mm) and parallel to the first support,and (8) imaging the sample to detect bound labeled imager strands.

2. Software for Control of Fluidic Steps

In some embodiments, all fluidic exchange steps are performed using afluidic system comprising electronic, and/or pneumatic, and/orhydraulic, and/or electro-fluidic actuators and systems. In certainsituations, the fluidic system is controlled by software. In someembodiments, wherein the fluidic system is automatically controlled bysoftware synchronizing steps (1 (contacting a sample withtarget-specific binding partners) and/or 2 (optionally removing unboundtarget-specific binding partners) and/or 3 (increasing the number ofdocking strands, or amplification) and/or 4 (contacting the sample withlabeled imager strands capable of binding a docking strand, directly orindirectly) and/or 5 (optionally removing unbound labeled imagerstrands), and/or 7 (optionally removing the bound labeled imager strandsfrom the docking strands) with the imaging step (6).

In some embodiments, the fluidic system is controlled by softwaresynchronizing the steps (1 and/or 2 and/or 3 and/or 4 and/or 5, and/or7) with the imaging step (6) by communicating with the imaging software,with the references to step numbers described in the precedingparagraph.

In some embodiments, all fluidic steps are performed while the sample ison the imaging device. In some embodiments, steps 4, 5, and 7 areperformed while the sample is on the imaging device, with the referencesto step numbers described two paragraphs previously.

The sample may be fixed in a disposable imaging chamber (such as a flowcell) or a reusable imaging chamber (such as a flow cell).

H. Kits

In some embodiments, a composition comprises (1) one or more reagent(s)including but not limited to target-specific binding partners linked todocking-strands, wherein target-specific binding partners of differentspecificity are linked to different docking strands, labeled imagerstrands, buffers, amplification reagents, and/or reagents to removebound imager strands, (2) a fluidic system to perform all fluid exchangesteps, a software to control the fluidic system and time and/orsynchronize the fluidic steps with the imaging steps, (3) an imagingchamber (such as a flow cell) to affix on the sample of interest with atleast one optically transparent side to allow imaging of the sample. Insome embodiments, the imaging chamber (such as a flow cell) isdisposable.

II. Components of the Method

A. Target-Specific Binding Partners

The target recognition moiety refers to antibodies and antibody-likemolecules that can be used to detect the target molecule. Antibodyrefers to any immunoglobulin from any species that can specificallyrecognize a target molecule. Antibody-like molecule refers to (Class A)any engineered variation or fragment of an antibody such as Fab, Fab′,F(ab′)₂, single heavy chain, diabody, and the like (antigen bindingfragments of antibodies) (Class B) any known binding partner of a targetmolecule and engineered variants of such binding partner, (Class C) anybinding partner of the target molecule engineered via directed evolution(e.g., peptides and aptamers), and (Class D) any molecule thatselectively forms covalent bond(s) with a target (e.g., a suicidesubstrate of an enzyme of interest).

The target-specific binding partner may be provided in a liquid mediumor buffer solution.

Table 3 provides a representative listing of targets and correspondingtarget recognition moieties.

TABLE 3 Representative Targets and Target Recognition Moieties TargetRecognition Target Moiety Source or Sequence Any protein Antibody (ClassA) Variable Fluorescein Antibody (Class A) Abcam, product # (chemicalcompound) ab7253 Digoxigenin Antibody (Class A) Abcam, product #(chemical compound) ab76907 Biotin Avidin/Streptavidin (Class B)Epidermal growth Epidermal growth factor receptor factor (EGF, Class B)(EGFR, protein) Platelet-derived Platelet-derived growth factor growthfactor receptor (PDGFR, (PDGF, Class B) protein) Epidermal growth E07aptamer Li et al., PloS ONE, factor receptor (Class C) 2011; 6(6):e20299 (EGFR, protein) Integrins (protein) RGD-containing peptides(Class B) TNF-α (protein) T09.12 peptide Xu et al., Chem Biol. (Class C)2002 August; 9(8): 933-42. HaloTag (enzyme) Halogenated Bioconjug Chem.2015 compounds (Class D) Jun. 17; 26(6): 975-86. Oxidosqualene[3H]29-methylidene- Biochem Biophys Res cyclase (OSC, 2,3-oxidosqualeneCommun. 1992 Aug. enzyme) ([3H]29-MOS, 31; 187(1): 32-8. Class D)

Table 4 provides a listing of additional targets. Antibodies and otherknown binding partners of these targets may be used as targetrecognizing moieties.

TABLE 4 Additional Representative Targets   Actin AIF AKTalpha-synuclein amyloid precursor protein annexin arrestin BAD BAX Bcl-2Bcl-2 beta-catenin BRCA1 cAMP caveolin CD20 CD3 CD4 CD45 CD68 CD8collagen CREB DNA E-Cadherin EGFR EpCAM ER ERK ERK FOXA FOXP3 GABA GAPDHGFP granzymeB GRB2 HER2 HER3 HIF-1 histoneH3 H5P27 HSP70 HSP90 keratinKi67 lamin MAPK MEK MET MMP mTOR MYC NeuN p21 p53 PAX PD-1 PD-L1 PI3K PRPSD95 RAS SOX STAT synapsin Tau TOM20 tubulin ubiquitin VEGF vimentinWNT

B. Docking Strands

In some embodiments, the docking moiety or docking strand is a nucleicacid, a protein, a peptide, or a chemical compound. Many proteins anddomains of proteins are known to interact with other proteins, domainsor peptides. Some of the best-known domains include SH2, SH3, and WD40domains. In many cases the binding partner of these proteins and domainsare known and can be engineered to have the desired affinity. Forexample, biotin and avidin/streptavidin interact with sufficientspecificity. Many other chemical compounds, such as digoxigenin,fluorescein, tacrolimus and rapamycin also have well known bindingpartners.

In some embodiments, the docking strand comprises nucleic acids. In someembodiments, the nucleic acids are single stranded nucleic acids such assingle stranded DNA, RNA, or a nucleic acid analog. A nucleic acidanalog (also known as non-natural nucleic acid) may include an alteredphosphate backbone, an altered pentose sugar, and/or alterednucleobases. Nucleic acid analogs may include, but are not limited to,2′-O-Methyl ribonucleic acid, 2′-fluoro ribonucleic acid, peptidenucleic acid, morpholino and locked nucleic acid, glycol nucleic acid,and threose nucleic acid.

In some embodiments, the docking strand is attached to the imager strandcovalently and in other embodiments noncovalently.

In some embodiments, the docking strand comprises single-strandednucleic acids and may be from about 5 to 20 nucleotides long, from about8 to 15, or from about 10 to 12 nucleotides long. In some embodiments,the docking strand is about 5, 8, 9, 10, 11, 12, 13, 14, 15, 18, or 20nucleotides long.

The docking strand may be an independent element or it may be part ofthe target recognizing moiety. For example, if the target recognizingmoiety is an antibody, part of the Fc domain of the antibody may be thedocking strand and a peptide or protein that binds the Fc domain may beused, such as protein A or protein G.

The docking strand may be provided in a liquid medium or buffersolution.

C. Imager Strands

In some embodiments, the docking strand may be a nucleic acid strand. Insuch cases, the observable moiety or label may be conjugated to animager moiety, which may be a nucleic acid strand that is complementaryto the docking strand. In other words, the imager strand specificallybinds the docking strand. In such a case, the label may be conjugated toan imager moiety that may be from about 5 to 20 nucleotides long, fromabout 8 to 15, or from about 10 to 12 nucleotides long. In someembodiments, the imager moiety is about 5, 8, 9, 10, 11, 12, 13, 14, 15,18, or 20 nucleotides long.

In some embodiments, the imager strand is even longer, such as from 20to 80 nucleotides long, for example less than or equal to 80, 75, 70,65, 60, 55, 50, 45, 40, 35, or 30 nucleotides long. In embodimentsemploying a hairpin structure for the imager strand, the length of theimager strand may be longer than if no hairpin structure is used.

In some embodiments, the complementary portions between the imagermoiety and the docking strand may be from about 5 to 20 nucleotideslong, from about 8 to 15, or from about 10 to 12 nucleotides long. Insome embodiments, the complementary portions between the imager moietyand the docking strand may be about 5, 8, 9, 10, 11, 12, 13, 14, 15, 18,or 20 nucleotides long.

In some embodiments, the nucleic acid imager strand comprises singlestranded nucleic acids such as single stranded DNA, RNA, or a nucleicacid analog. A nucleic acid analog (also known as non-natural nucleicacid) may include an altered phosphate backbone, an altered pentosesugar, and/or altered nucleobases. Nucleic acid analogs may include, butare not limited to, 2′-O-Methyl ribonucleic acid, 2′-fluoro ribonucleicacid, peptide nucleic acid, morpholino and locked nucleic acid, glycolnucleic acid, and threose nucleic acid.

In some embodiments, the imager moiety is a protein, peptide, or achemical compound, as a partner to the docking strand options discussedabove in Section II.B above.

In some embodiments, the docking strand may bind to the imager moietyindirectly, such as through an intermediate moiety. For instance, whenthe docking strand and the imager moiety are nucleic acids, anintermediate moiety comprising nucleic acids may be used as long as theintermediate moiety has a first region complementary to the dockingstrand and a second region complementary to the imager moiety. In thisembodiment, it is not necessary for the docking strand to becomplementary to the imager moiety. The intermediate moiety may serveonly a bridging function or it may also serve an amplification function.

The imager strand may be provided in a liquid medium or buffer solution.

D. Primer Strands

In some instances, the target-specific binding partner is linkedindirectly to a docking strand, such as through a primer. For instance,when the docking moiety and the imager moiety comprise nucleic acids,the primer strand comprising nucleic acids may be used as a bindinglocation for the docking strand (if the docking strand has a regioncomplementary to the primer strand) or it may be used as a primer fornucleic acid synthesis through, for example, rolling circleamplification. The primer strand may also be used to initiate thecascade of binding events in hybridization chain reaction amplification.In instances where the primer serves as a location for amplification(such as rolling circle amplification, hybridization chain reactionamplification), the primer is not necessarily complementary to thedocking strand. Instead, it serves as a template for amplification andthe docking strands are included through the amplification process.

In some embodiments, the target-specific binding partner and linkedprimer are added to the sample as a first step, docking strand added asa second step, and imager strand added as a third step. In anotherembodiment, the components are not added in discrete steps. Washingsteps may be added between the first, second, and/or third steps.

In some embodiments, the primer strand comprises nucleic acids. In someembodiments, the nucleic acids are single stranded nucleic acids such assingle stranded DNA, RNA, or a nucleic acid analog. A nucleic acidanalog (also known as non-natural nucleic acid) may include an alteredphosphate backbone, an altered pentose sugar, and/or alterednucleobases. Nucleic acid analogs may include, but are not limited to,2′-O-Methyl ribonucleic acid, 2′-fluoro ribonucleic acid, peptidenucleic acid, morpholino and locked nucleic acid, glycol nucleic acid,and threose nucleic acid.

In some embodiments, the primer strand comprises single-stranded nucleicacids and may be from about 5 to 20 nucleotides long, from about 8 to15, or from about 10 to 12 nucleotides long. In some embodiments, theprimer strand is about 5, 8, 9, 10, 11, 12, 13, 14, 15, 18, 20, 25, 30,35, 40, 45, 50, 55, 60, 65, or 70 nucleotides long.

The primer strand may be provided in a liquid medium or buffer solution.

E. Intermediate Strands

In some instances, the docking strand binds to the imager strand throughan intermediate moiety (or intermediate strand). For instance, when thedocking moiety and the imager moiety comprise nucleic acids, theintermediate strand comprising nucleic acids may be used as long as theintermediate strand has a first region complementary to the dockingstrand and a second region complementary to the imager strand. In suchembodiments, it is not necessary for the docking strand to becomplementary to the imager moiety.

In some embodiments, the intermediate strand is added as a first step toa sample comprising the target-specific binding partner linked to adocking strand, either directly or indirectly, and the imager strandsadded as a second step. In another embodiment, the intermediate strandand imager strand are not added in discrete steps. In some instances,the intermediate strand and imager strand are hybridized together beforebeing added in a single step.

In some embodiments, the intermediate strand comprises nucleic acids. Insome embodiments, the nucleic acids are single stranded nucleic acidssuch as single stranded DNA, RNA, or a nucleic acid analog. A nucleicacid analog (also known as non-natural nucleic acid) may include analtered phosphate backbone, an altered pentose sugar, and/or alterednucleobases. Nucleic acid analogs may include, but are not limited to,2′-O-Methyl ribonucleic acid, 2′-fluoro ribonucleic acid, peptidenucleic acid, morpholino and locked nucleic acid, glycol nucleic acid,and threose nucleic acid.

In some embodiments, the intermediate strand comprises single-strandednucleic acids and may be from about 5 to 30 nucleotides long, from about8 to 15, or from about 10 to 12 nucleotides long. In some embodiments,the intermediate strand is about 5, 8, 9, 10, 11, 12, 13, 14, 15, 18,20, 25, or 30 nucleotides long.

The intermediate strand may be provided in a liquid medium or buffersolution.

F. Nucleic Acids in Hairpin Format

Any of the linear nucleic acids described herein may optionally beprovided in a hairpin format. This includes the imager strand, dockingstrand, primer strand, and intermediate strand. In the hairpin format, aregion of from at least 1-5 nucleotides at the end of the hairpin stemregion may optionally comprise only G's and C's. This G/C region isknown as a clamp. The G/C region prevents or reduces fraying at the endof the hairpin to prevent opening up into linear DNA.

A hairpin may be used in contexts when a user desires to break theinteraction (direct or indirect) between the imager strand and thedocking strand using a polymerase with a strand-displacement activity(e.g., phi29) or a polymerase with a 5′-to-3′ exonuclease activity(e.g., DNA Polymerase I). A hairpin may also be used to limit unwantedbinding of single-stranded nucleic acids.

G. Labels

Various labels, also known as observable moieties, may be bound to theimager strand. These labels or observable moieties assist the user byenabling detection of the bound imager strand. When the applicationrefers to detecting bound labeled imager strands, the applicationreferences detecting the signal produced by the label or observablemoiety bound to the imager strand.

In some embodiments, any observable moiety may be employed and, in someembodiments, the moiety is optically observable. The moiety may besignal absorbing or signal emitting. Of signal emitting molecules,molecules that fluoresce may be used, such as organic small molecules,including, but not limited to fluorophores, such as, but not limited to,fluorescein, Rhodamine, cyanine dyes, Alexa dyes, DyLight dyes, Attodyes, etc.

In some embodiments, organic polymers, such as p-dots may be employed.In some embodiments, the observable moiety may be a biological molecule,including but not limited to a fluorescent protein or fluorescentnucleic acid (including fluorescent RNAs including Spinach and itsderivatives). In some embodiments, the observable moiety may be aninorganic moiety including Q-dots. In some embodiments, the observablemoiety may be a moiety that operates through scattering, either elasticor inelastic scattering, such as nanoparticles and Surface EnhancedRaman Spectroscopy (SERS) reporters (e.g., 4-Mercaptobenzoic acid,2,7-mercapto-4-methylcoumarin). In some embodiments, the observablemoiety may be chemiluminescence/electrochemiluminescence emitters suchas ruthenium complexes and luciferases. The observable moiety maygenerate an optical signal, an electromagnetic signal (across the entireelectromagnetic spectrum), atomic/molecular mass (e.g. detectable bymass spectrometry), tangible mass (e.g., detectable by atomic forcemicroscope), current or voltage.

EXAMPLES Example 1: Multiple Modes of Amplification

There are multiple approaches to amplification. This exampledemonstrates the use of three approaches including enzymaticamplification using HRP conjugates (FIG. 7A-C), rolling circleamplification (FIG. 7D-E), and hybridization chain reaction (HCR) (FIG.7F-G).

For HRP-based amplification, formalin-fixed paraffin-embedded (FFPE)tonsil tissue sections were dewaxed and antigen-retrieved using R-BufferA (Fisher Scientific) in a Lab Vision PT-module. Tissue sections wereblocked in 3% BSA and 0.2% Triton-X 100 for 1.5 hours. Tissue sectionswere stained with a mouse anti-cytokeratin primary antibody overnight at4° C. in a humidity chamber. Tissue sections were then washed with1×PBS, and stained for 2 hours at room temperature with a goatanti-mouse secondary antibody conjugated to a DNA docking strand (D1).Tissue sections were washed again in 1×PBS, and stained for DAPI.

A fluorescence microscope was used to image the tissue section in theDAPI and Cy5 channels to serve as a blank. An imager strand (11-650),comprising a red fluorophore attached to DNA that includes a domaincomplementary to a docking strand D1, was added to the prepared tissuesection and allowed to hybridize for 25 minutes at room temperature.Sections were washed to remove unbound 11-650. Then, fluorescence imageswere captured in the DAPI and Cy5 channels using a 10× objective. SeeFIG. 7B.

The imager strand 11-650 was then removed by applying 10 units of USERenzyme to the tissue sections for 15 minutes at room temperature,washing with 1×PBS, incubating the tissue sample with 30% formamide for5 minutes, then washing with 1×PBS. A fluorescence microscope was usedto confirm the complete removal of fluorescent signal in the Cy5channel. Then a brightfield image was taken at 10× magnification as ablank.

To amplify the cytokeratin signal for brightfield immunohistochemicaldetection, the tissue section was incubated with an imager strand(I1-HRP), comprising a horseradish peroxidase (HRP) enzyme attached toDNA that includes a domain complementary to docking strand D1. Thesample was washed by submerging the tissue section in 1×PBS. Then,chromogenic signal amplification was carried out by applying a solutionof 3,3′-diaminobenzidine (DAB) chromogen to the sample for 10 minutes.The sample was washed in 1×PBS. Finally, the sample was imaged usingbrightfield illumination. FIG. 7C.

FIG. 7A-C illustrate the use of DNA Exchange to enable fluorescence andbrightfield (e g immunohistochemistry) images to be captured on the samesample. While this example demonstrates the use of HRP-conjugated imagerstrands for chromogenic signal amplification, HRP-conjugated imagerstrands could also be applied for fluorescent signal amplification usingalternative enzyme substrates (e.g. tyramide).

In a separate approach for amplification based on rolling circleamplification, cultured HeLa cells were fixed with warm 3%paraformaldehyde and 0.1% glutaraldehyde, reduced with 0.1% sodiumborohydride, blocked and permeabilized with 3% bovine serum albumin and0.2% Triton-X 100, and then stained with a rabbit primary antibodyagainst vimentin overnight.

For a control sample, a goat-anti-rabbit antibody conjugated to adocking strand (Gt-a-Rb-D1) was incubated with the cells for 2 hours atroom temperature as a secondary staining step. After washing the controlsample, DAPI and 100 nM fluorescently labeled imager strands were addedto the sample. Fluorescence images in the DAPI and Cy5 channels werecollected of the control well. FIG. 7D.

The following procedure was carried out for cell samples undergoingrolling circle amplification. A goat-anti-rabbit antibody conjugated toa docking strand (Gt-a-Rb-D1), was used as a template for ligation. Aligation solution was made in a PCR tube with 125 nM circle oligo (IDTDNA), 125 nM Gt-a-Rb-D1, 20 U/μL T4 ligase (NEB), in 1× ligation buffer(NEB). The ligation solution was incubated at room temperature for twohours. After ligation, the ligation solution was diluted 1:5 in blockingbuffer, added to the cell samples, and allowed to incubate for 2 hoursat room temperature, then washed in 1×PBS.

In a separate vessel, a polymerase solution was made containing 0.1mg/mL BSA, 0.2 mM dNTPs, and 1 U/μL phi29 DNA Polymerase in 1×polymerase reaction buffer (New England Biolabs). The polymerasesolution was applied directly the cell samples that were prepared forRCA. The samples were incubated with the polymerase solution for 1.5hours at 30° C. The cell samples were washed three times with 1×PBS.DAPI was added to stain the cell nuclei. Finally, 100 nM fluorescentlylabeled imager strands were added prior to imaging. Fluorescence imagesin the DAPI and Cy5 channels were collected following RCA. See FIG. 7E.

In a separate approach for amplification based on a hybridization chainreaction, formalin-fixed paraffin-embedded (FFPE) tonsil tissue sectionswere dewaxed and antigen-retrieved using R-Buffer A (Fisher Scientific)in a Lab Vision PT-module. Tissue sections were blocked in 3% BSA and0.2% Triton-X 100 for 1.5 hours. Tissue sections were stained with amouse anti-cytokeratin primary antibody overnight at 4° C. in a humiditychamber. Tissue sections were then washed with 1×PBS, and stained for 2hours at room temperature with a goat anti-mouse secondary antibodyconjugated to a DNA docking strand (D1). Tissue sections were washedagain in 1×PBS, and stained for DAPI.

A fluorescence microscope was used to image the tissue section in theDAPI and Cy5 channels to serve as a blank. An imager strand (I1-650),comprising a red fluorophore attached to DNA that includes a domaincomplementary to a docking strand D1, was added to the prepared tissuesection and allowed to hybridize for 25 minutes at room temperature.Sections were washed to remove unbound I1-650. Then, fluorescence imageswere captured in the DAPI and Cy5 channels using a 10× objective. SeeFIG. 7F.

The imager strand I1-650 was then removed by applying 10 units of USERenzyme to the tissue sections for 15 minutes at room temperature,washing with 1×PBS. A fluorescence microscope was used to confirm thecomplete removal of fluorescent signal in the Cy5 channel (data notshown).

After removal of the imager strand, a primer strand including the I1sequence was hybridized to the D1 docking strand (20 nM) for 30 minutesat room temperature. The sections were washed with 1×PBS to wash theunbound primer strands. In parallel, hairpin strands H1 and H2-D2 werediluted to 1 uM in 5×SSX in separate microcentrifuge tubes. The tubeswere heated and held at 90° C. for 5 minutes, and then slowly cooleddown to room temperature. The hairpins were then pooled and diluted to200 nM in 5×SSC with 0.1% Tween 20 and 10% dextran sulfate. Thissolution was added to the tissue section and incubated overnight in anincubation chamber at room temperature. The sections were then washedwith PBS 1× Finally, 100 nM fluorescently labeled imager strands I2 wereadded prior to imaging. Fluorescence images in the DAPI and Cy5 channelswere collected following HCR amplification. FIG. 7G, right.

Example 2: Amplification with Pre-Ligated Circle Oligo

Nonlinear DNA strands were made in advance of performing an assay. Usingnonlinear DNA strands provides the benefit that it may increase theefficiency of signal amplification, particularly if the signalamplification method used is similar to rolling circle amplification(FIG. 8). In this example, a circular DNA strand was made via a ligationstep. The DNA sequence used in the ligation step was referred to as thecircle oligo, which includes a domain that is equivalent to an imagerstrand sequence (i.e. complementary to a docking strand).

Cultured HeLa cells were fixed with warm 3% paraformaldehyde and 0.1%glutaraldehyde, reduced with 0.1% sodium borohydride, blocked andpermeabilized with 3% bovine serum albumin and 0.2% Triton-X 100, andthen stained with a rabbit primary antibody against vimentin overnight.A goat-anti-rabbit antibody conjugated to a docking strand (Gt-a-Rb-D1),was then used as a secondary stain and allowed to incubate for 2 hoursat room temperature.

A ligation solution was made in a PCR tube with 0.5 μM circle oligo (IDTDNA), 50 μM ATP, 2.5 mM MnCl₂, 5 U/μL CircLigase (Cat #CL4111K,EpiCentre), in 1× reaction buffer (EpiCentre). The ligation solution wasplaced in a thermocycler for 1 hour to incubate at 60° C. Afterligation, a 1:4 dilution of the ligation solution was made in blockingbuffer, added to the stained cell samples, and allowed to incubate for25 minutes to hybridize to a docking strand on an antibody-labeledtarget complex before washing in PBS.

As an alternative approach, the ligation step can be carried out priorto staining the sample with a secondary antibody conjugate. Followingthe ligation step, an excess of ligation solution was hybridized to anantibody DNA conjugate such that the molar ratio of ligated circle oligowas at least two-fold greater than the molar ratio of docking strandsbound to the antibody. After hybridization of the ligated circle oligoto Gt-a-Rb-D1, the complex was added to the sample and incubated for twohours at room temperature as a secondary staining step, then washedthree times in 1×PBS.

In a separate vessel, a polymerase solution was made containing 0.1mg/mL BSA, 0.2 mM dNTPs, and 1 U/μL phi29 DNA Polymerase in 1×polymerase reaction buffer (New England Biolabs). The polymerasesolution was applied directly to a fixed cell sample that was alreadystained with a primary antibody, a secondary antibody docking strandconjugate, and hybridized to a ligated circle oligo. The sample wasincubated with the polymerase solution for 1.5 hours at 30° C. The cellsamples were washed three times with 1×PBS. DAPI was added to stain thecell nuclei. Finally, 100 nM fluorescently labeled imager strands wereadded prior to imaging. FIG. 8 shows the use of pre-formed nonlinear DNAstrands that can be hybridized to docking strands as a starting pointfor rolling circle polymerization.

Example 3: Sample Re-Interrogation (0-A-0-A)

This example demonstrates the ability to use Exchange Imaging toreinterrogate a target in a sample. It also shows that the enzymaticmethod of extinguishing signal does not affect, modify, or degrade thestaining of the sample.

In this example, docking strands (D1 and D2) were conjugated tosecondary antibodies goat anti-mouse and goat anti-rabbit respectively.The imagers strands I1U and I2U, respectively complementary to D1 andD2, were labeled with a fluorescent dye (ATTO647N). The sequence of theimager strands I1U and I2U includes several uracil nucleobases. Anenzyme, or cocktail of enzymes, can cleave bases leading to thedehybridization of the docking-imager duplex, leading to a decrease inthe observed signal.

Cultured HeLa cells were fixed with warm 3% paraformaldehyde and 0.1%glutaraldehyde, reduced with 0.1% sodium borohydride, blocked andpermeabilized with 3% bovine serum albumin and 0.2% Triton-X 100 in1×PBS for 1.5 hours. The cells were first stained using a cocktail ofprimary antibodies anti-tubulin and anti-TOM20, raised in mouse andrabbit respectively, overnight at 4° C. Goat secondary antibodiesagainst mouse and rabbit conjugated to two different docking strands(Gt-a-Ms-D1 and Gt-a-Rb-D2) were used for a secondary staining for 2hours at room temperature. DAPI was added to stain the cell nuclei.

Samples were loaded onto an inverted Nikon Eclipse Ti microscope (NikonInstruments) with a fluorescence module and an Andor Zyla sCMOS camera.The microscope was equipped with two fluorescence filter sets to imageDAPI and the fluorescently labeled imager strands (Cy5 channel).

The sample was first imaged using a 20× dry objective (Nikon, 0.45 NA),in both DAPI and Cy5 channels to register the cells using DAPI, and tomeasure the autofluorescence signal in the Cy5 channel (FIG. 9A). Asolution of 100 nM I1U was added to the sample and incubated for 15minutes. The sample was then washed 3 times with 1×PBS, and imaged again(FIG. 9B). To extinguish the signal, a solution containing 5 units ofUSER™, 50 mM potassium acetate, 20 mM tris-acetate, 10 mM magnesiumacetate, and 100 μg/ml BSA, was added to the sample, and incubated atroom temperature for 15 minutes. The sample was then washed 3 times withPBS 1×, and imaged (FIG. 9C). A solution of 100 nM I2U was added to thesample and incubated for 15 minutes. The sample was then washed 3 timeswith 1×PBS, and imaged (FIG. 9D). The signal was extinguished aspreviously, and the sample was imaged again (FIG. 9E). Finally, asolution of 100 nM I1U was added to the sample and incubated for 15minutes. The sample was washed 3 times with 1×PBS, and imaged (FIG. 9F).

FIG. 9 shows the series of images obtained in the Cy5 channel duringthis experiment. In FIGS. 9A, 8C, and 8E, no signal is observed. Theseimages correspond to: before introduction of imager strand, afterremoval of I1U, and after removal of I2U respectively. After addition ofthe imager strand I1U, the microtubule networked is observed (FIG. 8B,8F). FIG. 8D shows the presence of mitochondria after adding I2U. FIG.9G presents the average signal intensity in the images of FIGS. 9A-F.The signal decreases by more than 98% in both cases shown in FIGS. 9Cand 8E. The signal recovery on the microtubule target after two roundsof exchange is over 95%, demonstrating the ability to reliablyreinterrogate a target after multiple exchange steps.

The images in FIGS. 9A-F were obtained by manually pipetting theincubation and wash solutions in and out of the imaging chambers. TheExchange Imaging workflow can be automated by using flow cells and afluidic system.

Using a fluidics system synchronized with the acquisition software ofthe microscope, the fluidics steps required for the hybridization of theimager strand (injections, incubation, washes), as well as the signalremoval can be automatically performed between imaging rounds.

HeLa cells were cultured, fixed, and stained as described above, in aflow cell, which can be fitted on a regular microscope stage. The samplewas first imaged using a 20× dry objective (Nikon, 0.45 NA), in bothDAPI and Cy5 channels to register the cells using DAPI, and to measurethe autofluorescence signal in the Cy5 channel (FIG. 9, Image H). Asolution of 100 nM I1U was flowed into the sample chamber and incubatedfor 15 minutes. The sample was then washed with 1×PBS with continuousflow for 30 seconds, and imaged again (FIG. 91). Next, a solutioncontaining 5 units of USER™, 50 mM potassium acetate, 20 mMtris-acetate, 10 mM magnesium acetate, and 100 μg/ml BSA, was injectedinto the flow cell, and incubated for 15 minutes. The sample was thenwashed for 30 seconds with PBS 1×, and imaged (FIG. 9J) Finally, thesolution of imager I1U was injected again into the flow cell, incubatedfor 15 minutes, washed with PBS for 30 seconds. The sample was imagedone last time (FIG. 9K).

Example 4: Proximity Detection with Stable Binding

A pair of proximity probes (PL and PR) were conjugated to anti-mouseantibodies using the ThunderLink kit (Innova Biosciences). Cultured HeLacells were fixed with warm 3% paraformaldehyde and 0.1% glutaraldehyde,reduced with 0.1% sodium borohydride, blocked and permeabilized with 3%bovine serum albumin and 0.2% Triton-X 100, and then stained with amouse primary antibody against alpha-tubulin. Fixed cells were thenstained with a mixture of PL- and PR-conjugated secondary antibodies,and washed to remove any unbound material. A large fraction ofanti-alpha-tubulin antibodies in the sample should receive at least onemolecule of PL-conjugated secondary antibody and at least one moleculeof PR-conjugated antibody. To detect proximity signal, DAPI and 100 nMof imager strand was added to the sample, and the sample was imaged withwide-field fluorescence microscope at 20×, with an LED light source(FIG. 10A (top panel)).

In a negative control experiment (FIG. 10, bottom panel), one of theproximity probes was conjugated to an off-target, anti-rabbit secondaryantibody. Fixed cells were stained with mouse anti-tubulin primary,PL-conjugated anti-mouse and PR-conjugated anti-rabbit secondaryantibodies. The anti-rabbit secondary antibody should not bind to themouse derived primary, and thus the proximity probes should not beco-localized and the full docking site will not be available to bind theimager strand.

As shown in FIG. 10 the microtubule structures are apparent only whenboth proximity probes are specifically bound to the target. Fluorescencesignal is stable for standard fluorescence imaging.

Example 5: Control Experiment for Off-Target Crossreactivity

Cross-reactivity between off-target imager and docking strands wasassessed by measuring the signal intensity of a sample before and afterexposure to noncomplementary imager strand sequences.

Cultured HeLa cells were fixed, reduced, blocked and permeabilized, thenstained with a mouse primary antibody against alpha-tubulin. Fixationbuffer was composed of 3% paraformaldehyde and 0.1% glutaraldehyde. Asolution containing 0.1% sodium borohydride was used to reduce fixedcells. A solution with 3% bovine serum albumin and 0.2% Triton-X 100 wasused to block and permeabilized cells for 1.5 hours, prior to overnightprimary antibody staining. To test the crossreactivity of docking strandA to imager strands B and C, anti-mouse antibodies conjugated to dockingstrand A (a-Ms-A_(d)) were added to fixed cell samples stained foralpha-tubulin. Secondary staining with a-Ms-A_(d) was done for 2 hoursat room temperature in blocking buffer, then washed three times in1×PBS. DAPI stain was added to all wells, and blank images were taken inboth the DAPI and Cy5 channels on a Nikon fluorescence microscope with a20× objective.

After recording blank images, imager strand solutions were prepared. Inthis example, an imager strand was partially double stranded; the imagerstrand was composed of a universal domain and a non-universal domain,where the universal domain is hybridized a complementary sequence thatis attached to a fluorophore and the non-universal domain is singlestranded and available to interact with a docking strand in a sample. Inthis example, a fluorophore is included in the imager strand indirectly,through a DNA-based bridge. In this example, the non-universal domain inan imager strand is complementary to a specific docking strand (ex.docking strand A, B, or C.)

A 100 nM solution of imager strands A (A_(i)), B (B_(i)), or C (C_(i))was added to separate sample wells and allowed to hybridize for 10minutes. Following hybridization of the imager strands, samples werewashed with 1×PBS three times. Images were taken of each well in boththe DAPI and Cy5 channels on a Nikon fluorescence microscope with a 20×objective. The same field of view was imaged as selected for the blankimage previously.

The signal intensity of each sample was compared before and afteraddition of the imager strand using custom made software. Images werealigned using the DAPI channel, and a mask was made to segmentindividual cells from the background. The mean fluorescence intensityinside the cell region was calculated for the Cy5 channel and divided bythe mean intensity of the background to yield a signal-to-noise ratio.The signal-to-noise ratios obtained in the blank image were compared tothe signal-to-noise ratios obtained post-addition of imager strand toassess cross-reactivity between imager strands A_(i), B_(i), and C_(i)with docking strand A.

As shown in FIG. 11, the on-target imager strand Ai clearly shows thespecific microtubule structures stained with a-Ms-A_(d). FIG. 11 alsoshows that B_(i) does not crossreact with docking strand A, but C_(i)zdoes.

Example 6: USER and SubUSER

This example demonstrates the ability to extinguish signal from a targetusing enzymatic activity. In this example, the docking strand (D1) wasconjugated to secondary antibodies goat anti-mouse. The imagers strandsI1U complementary to D1, were labeled with a fluorescent dye (ATTO647N).The imager strand I1U contained several uracil nucleobases that can becleaved by specific enzymatic activity, destabilizing the dupleximager/docking strands, resulting in the removal of fluorescent signal.

Cultured HeLa cells were fixed with warm 3% paraformaldehyde and 0.1%glutaraldehyde, reduced with 0.1% sodium borohydride, blocked andpermeabilized with 3% bovine serum albumin and 0.2% Triton-X 100 in1×PBS for 1.5 hours. The cells were first stained with a primaryantibody anti-tubulin raised in mouse, overnight at 4° C. Secondarystaining was performed using a goat secondary antibody against mouseconjugated to D1 for 2 hours at room temperature. DAPI was added tostain the cell nuclei.

Samples were loaded onto an inverted Nikon Eclipse Ti microscope (NikonInstruments) with a fluorescence module and an Andor Zyla sCMOS camera.The microscope was equipped with two fluorescence filter sets to imageDAPI and the fluorescently labeled imager strands (Cy5 channel).

A solution of 100 nM I1U was added to two separate samples and incubatedfor 15 minutes. The samples were then washed 3 times with 1×PBS, andimaged using a 20× dry objective (Nikon, 0.45 NA), in both DAPI and Cy5channels (FIG. 12, Image A and C). To extinguish the signal, a solutioncontaining 2 units of USER™, 50 mM potassium acetate, 20 mMtris-acetate, 10 mM magnesium acetate, and 100 μg/ml BSA, was added toone sample. To the other sample, a solution of 10 units Uracil-DNAGlycosylase (UDG) in 20 mM Tris-HCl, 1 mM DTT, 1 mM EDTA. Both sampleswere incubated at room temperature for 15 minutes. The samples were thenwashed 3 times with PBS 1×, and imaged (FIG. 12, Image B for USER and Dfor UDG).

As shown on FIG. 12, signal can be almost completely extinguished eitherusing USER or UDG.

Example 7: Cleavage of Imager Strands by USER

As shown in FIG. 14, the extent that signal can be extinguished maydepend on the imager strand architecture and/or sequence design. In thisexample, formalin-fixed paraffin embedded (FFPE) tissue samples weredewaxed, antigen retrieved, blocked, and stained with anti-CD3antibodies conjugated to docking strand D1. The number of D1 dockingstrands bound to the sample were amplified by RCA and labeled withimager strands containing a domain complementary to D1 and linked to afluorophore. Imager strands either contained several uracil nucleobases(FIGS. 14A and C) or several uracil nucleobases and an abasic site(FIGS. 14B and D). Images were collected using a fluorescence microscopeto detect the presence of targets bound by labeled imager strands (FIG.14A-B).

To extinguish the signal, a solution containing USER was added andincubated with the tissue sample for 15 minutes, followed by washingsteps to remove the cleaved imager strands. Fluorescence images werecollected to confirm the removal of the fluorescence signal. As shown inFIG. 14D, the presence of an abasic site in addition to dideoxyuridinesin the imager strand sequence design results in improved removalefficiency compared with FIG. 14C.

Example 8: Combined Multicolor and Sequential Detection

This example illustrates the ability to use Exchange Imaging to detectmultiple targets using sets of imager strands functionalized withdifferent, spectrally separated fluorophores.

Formalin-fixed paraffin-embedded (FFPE) tonsil tissue samples weredewaxed, antigen retrieved, blocked, and stained with DAPI, as well asanti-CD4, anti-CD8, anti-Ki67, and anti-Cytokeratin antibodiesrespectively conjugated to docking strand D1, D2, D3, and D4. The numberof docking strands (D1, D2, D3, D4) bound to the sample via theantibodies was amplified by RCA. Imager strands I1, I2, I3, and I4,containing a domain complementary to D1, D2, D3, and D4 respectively,also comprised several uracil bases for enzymatic removal. I1, and 13are labeled with Atto565 dye, while I2 and I4 are labeled with Atto647N.Samples were imaged using an inverted Nikon Eclipse Ti microscope (NikonInstruments) with a fluorescence module and an Andor Zyla sCMOS camera.The microscope was equipped with fluorescence filter sets to image DAPIand the fluorescently labeled imager strands (TRITC and Cy5 channels).

In a first step, the sample was labeled using I1 and 12 imager strands,by incubating a cocktail of the two strands on the sample for 25minutes. The unbound strands were washed away, and images were collectedin the TRITC and Cy5 channels to detect the presence of the targetslabeled with the imager strands I1 and 12, respectively CD4 and CD8(FIGS. 15 B and C respectively). A DAPI image was also collected todetect the cell nuclei (FIG. 15 A).

The signal was then extinguished, using a solution containing USER,which was incubated with the tissue sample for 15 minutes, followed bywashing steps to remove the cleaved imager strands. Fluorescence imageswere collected to confirm the removal of the fluorescence signal.

Finally, the sample was labeled again using a cocktail solution of theimager strands I3 and I4, followed by a wash step to remove unboundimager strands. A fluorescence image was acquired in the TRITC and Cy5channels to detect the presence of Ki67 and Cytokeratin (FIGS. 15 E andF respectively). A DAPI image was also collected (FIG. 15 D), and usedto align and overlay the images of the four targets.

Example 9: Numbered Items

The following numbered items provide a further description of theembodiments herein and how they relate to each other.

Item 1. A method comprising

-   -   (1) contacting a sample being tested for the presence of one or        more targets with one or more target-specific binding partners,        wherein each target-specific binding partner is linked to a        nucleic acid strand and wherein target-specific binding partners        of different specificity are linked to different nucleic acid        strands,    -   (2) optionally removing unbound target-specific binding        partners,    -   (3) wherein the nucleic acid strand is a docking strand or a        primer strand and if the nucleic acid is        -   (a) a docking strand, increasing the number of docking            strands associated with each target-specific binding            partner, or        -   (b) a primer strand, associating more than one docking            strand with the primer strand,    -   (4) contacting the sample with labeled imager strands capable of        binding a docking strand, directly or indirectly,    -   (5) optionally removing unbound labeled imager strands,    -   (6) imaging the sample to detect bound labeled imager strands,    -   (7) optionally removing the bound labeled imager strands from        the docking strands, and    -   (8) optionally repeating steps (1)-(6), or any subset thereof.

Item 2. A method comprising

-   -   (1) contacting a sample being tested for the presence of one or        more targets with one or more target-specific binding partners,        wherein each target-specific binding partner is linked to a        nucleic acid strand and wherein target-specific binding partners        of different specificity are linked to different nucleic acid        strands,    -   (2) optionally removing unbound target-specific binding        partners,    -   (3) contacting the sample with labeled imager strands capable of        binding a docking strand, directly or indirectly, wherein the        nucleic acid strand in (1) is either a primer strand or a        docking strand and if the nucleic acid strand is a primer        strand, it is linked to a docking strand,    -   (4) optionally removing unbound labeled imager strands,    -   (5) imaging the sample to detect bound labeled imager strands        and determine if amplification (step (7)) is required,    -   (6) optionally removing the bound labeled imager strands from        the docking strands,    -   (7) optionally increasing the number of docking strands        associated with each target-specific binding partner, and    -   (8) optionally repeating steps (1)-(7), or any subset thereof.

Item 3. A method to test a sample for the presence of one or moretargets comprising

-   -   (1) contacting a sample being tested for the presence of one or        more targets with one or more target-specific binding partners,        wherein each target-specific binding partner is linked to a        nucleic acid strand and wherein target-specific binding partners        of different specificity are linked to different nucleic acid        strands,    -   (2) optionally removing unbound target-specific binding        partners,    -   (3) contacting the sample with a nonlinear amplifier strand        having complementarity to a nucleic acid strand, wherein the        nucleic acid strand is either a docking strand or a primer        strand,    -   (4) optionally removing unbound nonlinear amplifier strands,    -   (5) in either one or two steps amplifying the docking strand        with rolling circle amplification and contacting the sample with        labeled imager strands having complementarity to the docking        strand or amplified strand,    -   (6) imaging the sample to detect bound labeled imager strands,    -   (7) removing the bound labeled imager strands, and    -   (8) optionally repeating steps (1)-(8), or any subset thereof.

Item 4. The method of item 3, wherein a polymerase is used for rollingcircle amplification.

Item 5. The method of any one of items 3-4, wherein the nonlinearamplifier strand is combined with the target-specific binding partnerlinked to a nucleic acid strand before contacting the sample.

Item 6. The method of any one of items 3-5, wherein amplifying thedocking strand with rolling circle amplification occurs separately fromcontacting the sample with labeled imager strands having complementarityto the docking strand or amplified strand.

Item 7. The method of any one of items 3-6, wherein amplifying thedocking strand with rolling circle amplification occurs in the same stepas contacting the sample with labeled imager strands havingcomplementarity to the docking strand and wherein the imager strandoptionally comprises a 3′ modification to prevent amplification of theimager strand.

Item 8. The method of any one of items 3-5 or 7, wherein the imagerstrand is a circular imager strand for rolling circle amplification.

Item 9. The method of any one of items 3-7, wherein the imager strand isa linear imager strand that circularizes in the presence of the dockingstrand and a ligase.

Item 10. The method of any one of items 3-9, wherein the imager strandor amplifier strand comprises at least two regions that arecomplementary to the docking strand.

Item 11. The method of any one of items 3-10, wherein the labeled imagerstrands are linear strands.

Item 12. The method of any one of items 3-11, wherein the nonlinearamplifier strand is a circular strand.

Item 13. The method of any one of items 3-12, wherein the nonlinearamplifier strand becomes circular after ligation.

Item 14. A method to test a sample for the presence of one or moretargets comprising

-   -   (1) contacting the sample with one or more target-specific        binding partners, wherein each target-specific binding partner        is linked to a nucleic acid strand, directly or indirectly, and        wherein target-specific binding partners of different        specificity are linked to different nucleic acid strands,    -   (2) optionally removing unbound target-specific binding        partners,    -   (3) wherein the nucleic acid strand is a docking strand or a        primer strand and if the nucleic acid is        -   (a) a docking strand, optionally increasing the number of            docking strands associated with each target-specific binding            partner, or        -   (b) a primer strand, optionally associating more than one            docking strand with the primer strand,    -   (4) contacting the sample with labeled imager strands capable of        binding a docking strand, directly or indirectly,    -   (5) optionally removing unbound labeled imager strands,    -   (6) imaging the sample to detect bound labeled imager strands,        and    -   (7) optionally extinguishing signal from the bound labeled        imager strand;    -   (8) optionally repeating steps (1)-(7) or any subset thereof.

Item 15. The method of item 14, wherein the sample is mounted to anoptically transparent support.

Item 16. The method of any one of items 14-15, wherein after step (6)and after optionally performing step (7) the method further comprisesincreasing the number of docking strands associated with eachtarget-specific binding partner and repeating steps (4), optionally (5),(6), and optionally (7).

Item 17. The method of any one of items item 14-16, wherein the methodcomprises at step (3) increasing the number of docking strandsassociated with each target-specific binding partner or associating morethan one docking strand with the primer strand.

Item 18. The method of any one of items 1-17, where the increase in thenumber of docking strands associated with each target-specific bindingpartner is achieved using an enzyme and wherein the enzyme is optionallya polymerase.

Item 19. The method of any one of items 1-18, wherein enzymaticallycleaving, modifying, or degrading unbound labeled imager strands isachieved by using an enzyme and wherein the enzyme is optionally aglycosylase, a restriction endonuclease, a nicking endonuclease, anRNase, and an enzyme that cleaves at a non-natural nucleotide.

Item 20. A method to test a sample mounted to an optically transparentsupport for the presence of one or more targets comprising

-   -   (1) contacting the sample with one or more target-specific        binding partners, wherein each target-specific binding partner        is linked to a nucleic acid strand, and wherein target-specific        binding partners of different specificity are linked to        different nucleic acid strands,    -   (2) optionally removing unbound target-specific binding        partners,    -   (3) wherein the nucleic acid strand is a docking strand or a        primer strand and optionally if the nucleic acid is        -   (a) a docking strand, increasing the number of docking            strands associated with each target-specific binding            partner, or        -   (b) a primer strand, associating more than one docking            strand with the primer strand,    -   (4) contacting the sample with labeled imager strands capable of        binding a docking strand, directly or indirectly,    -   (5) optionally removing unbound labeled imager strands,    -   (6) optionally removing liquid to create a liquid-free sample,    -   (7) affixing a second optically-transparent material parallel to        the first support, and    -   (8) imaging the sample to detect bound labeled imager strands.

Item 21. The method of item 20, where the second optically-transparentmaterial is glass.

Item 22. The method of item 21, where the second optically-transparentmaterial is plastic.

Item 23. The method of any one of items 20-22, wherein the secondoptically-transparent material is 5 microns to 5 mm, from 50 microns to500 microns, or from 500 microns to 5 mm from the first support.

Item 24. The method of item 20, where the imaging is carried out with anupright microscope.

Item 25. A method to test a fixed sample mounted to an opticallytransparent support for the presence of one or more targets comprising

-   -   (1) contacting the sample with one or more target-specific        binding partners, wherein each target-specific binding partner        is linked to a nucleic acid strand and wherein target-specific        binding partners of different specificity are linked to        different nucleic acid strands,    -   (2) optionally removing unbound target-specific binding        partners,    -   (3) wherein the nucleic acid strand is a docking strand or a        primer strand and if the nucleic acid is        -   (a) a docking strand, increasing the number of docking            strands associated with each target-specific binding            partner, or        -   (b) a primer strand, associating more than one docking            strand with the primer strand,    -   (4) contacting the sample with labeled imager strands capable of        binding a docking strand, directly or indirectly,    -   (5) optionally removing unbound labeled imager strands,    -   (6) optionally removing liquid to create a liquid-free sample,    -   (7) affixing a second optically-transparent material parallel to        the first support, and    -   (8) imaging the sample to detect bound labeled imager strands.

Item 26. A method comprising

-   -   (1) contacting a sample being tested for the presence of one or        more targets with one or more target-specific binding partners,        wherein each target-specific binding partner is linked to a        nucleic acid strand and wherein target-specific binding partners        of different specificity are linked to different nucleic acid        strands,    -   (2) optionally removing unbound target-specific binding        partners,    -   (3) wherein the nucleic acid strand is a docking strand or a        primer strand and optionally if the nucleic acid is        -   (a) a docking strand, increasing the number of docking            strands associated with each target-specific binding            partner, or        -   (b) a primer strand, associating more than one docking            strand with the primer strand,    -   (4) contacting the sample with labeled imager strands capable of        binding a docking strand, directly or indirectly,    -   (5) optionally removing unbound labeled imager strands,    -   (6) imaging the sample to detect presence, location and number        of bound labeled imager strands,    -   (7) extinguishing signal from the bound labeled imager strand,        and    -   (8) repeating steps (3)-(6) or (3)-(7), with a labeled imager        strand optionally having a unique nucleotide sequence relative        to all other labeled imager strands.

Item 27. A composition comprising:

a sample bound to more than one target-specific binding partners, eachbinding partner bound to a nucleic acid strand and at least one dockingstrand stably bound to a labeled imager strand, directly or indirectly,wherein the nucleic acid strand is a docking strand or a primer strandif the nucleic acid is

-   -   (a) a docking strand, increasing the number of docking strands        associated with each target-specific binding partner, or    -   (b) a primer strand, associating more than one docking strand        with the primer strand.

Item 28. The composition of item 27, wherein the docking strand bound toa labeled imager strand, directly or indirectly, comprises at least 90%binding for 30 minutes.

Item 29. The composition of any one of items 27-28, wherein the

-   -   (a) docking strand or    -   (b) docking strand and any intermediate strand    -   is 80 nucleotides or less, 70, 60, 50, 40, or 30 nucleotides or        less.

Item 30. The composition of any one of items 27-29, wherein the imagerstrand is 60 nucleotides or less.

Item 31. A composition comprising:

-   -   (a) a composition employing a half-docking domain, wherein the        composition comprises (i) at least one first binding        partner-oligonucleotide conjugate comprising a binding partner        linked to an oligonucleotide that comprises a half-docking        domain, an optional stability domain, and optionally a spacer        domain; (ii) at least one second binding partner-oligonucleotide        conjugate comprising a binding partner linked to an        oligonucleotide that comprises a half-docking domain, an        optional stability domain, and optionally a spacer domain;        wherein the stability domains of (a) (i) and (a) (ii) are        complementary to each other, and wherein the half-docking        domains of (a) (i) and (a) (ii) combine linearly to form a full        docking domain; and (iii) at least one labeled imager strand or        intermediate strand comprising a 5′ domain, a 3′ domain, and a        linker domain located between the 5′ domain and the 3′ domain,        wherein the 5′ domain is complementary to the half-docking        domain of (a) (i) and the 3′ domain is complementary to the        half-docking domain of (a)(ii), and wherein the labeled imager        or intermediate strand is stably bound to the full docking        domain and if an intermediate strand is used also providing a        labeled imager strand; or    -   (b) a composition employing a half-primer domain, wherein the        composition comprises (i) at least one first binding        partner-oligonucleotide conjugate comprising a binding partner        linked to an oligonucleotide that comprises a half-primer        domain, an optional stability domain, and optionally a spacer        domain; (ii) at least one second binding partner-oligonucleotide        conjugate comprising a binding partner linked to an        oligonucleotide that comprises a half-primer domain, an optional        stability domain, and optionally a spacer domain; wherein the        stability domains of (b) (i) and (b) (ii) are complementary to        each other, and wherein the half-primer domains of (b) (i)        and (b) (ii) can combine linearly to form a full primer        domain; (iii) at least one docking strand capable of being        stably bound to the full primer domain; and (iv) at least one        labeled imager strand capable of being stably bound to the        docking strand or an intermediate strand capable of being stably        bound to the docking strand and a labeled imager strand capable        of being stably bound to the intermediate strand.

Item 32. The composition of item 31, wherein at least one imager strandis bound to a full docking domain for at least 30 minutes.

Item 33. The composition of item 31, wherein at least 70% of imagerstrands bound to full docking domains remain bound for at least 30minutes.

Item 34. The composition of item 31, wherein at least 90% of imagerstrands bound to full docking domains are resistant to non-enzymaticbuffer washes.

Item 35. A method to test a fixed sample mounted to an opticallytransparent support for the presence of one or more targets comprising

-   -   (1) contacting the sample with one or more target-specific        binding partners, wherein each target-specific binding partner        is linked to a nucleic acid strand and wherein target-specific        binding partners of different specificity are linked to        different nucleic acid strands,    -   (2) optionally removing unbound target-specific binding        partners,    -   (3) wherein the nucleic acid strand is a docking strand or a        primer strand and optionally if the nucleic acid is        -   (a) a docking strand, increasing the number of docking            strands associated with each target-specific binding            partner, or        -   (b) a primer strand, associating more than one docking            strand with the primer strand,    -   (4) contacting the sample with labeled imager strands capable of        binding a docking strand, directly or indirectly, wherein when        used indirect binding is capable of occurring through an        intermediate strand,    -   (5) optionally removing unbound labeled imager strands,    -   (6) imaging the sample to detect bound labeled imager strands,    -   (7) extinguishing signal from the bound labeled imager strand,    -   (8) contacting the sample with labeled imager strands having a        nucleotide sequence that is not complementary to a docking        strand or, when used, an intermediate strand,    -   (9) optionally removing unbound labeled imager strands,    -   (10) imaging the sample to detect bound labeled imager strands,        and    -   (11) optionally extinguishing signal from the bound labeled        imager strand.

Item 36. A method to test a fixed sample mounted to an opticallytransparent support for the presence of one or more targets comprising

-   -   (1) contacting the sample with one or more target-specific        binding partners, wherein each target-specific binding partner        is linked to a nucleic acid strand, and wherein target-specific        binding partners of different specificity are linked to        different nucleic acid strands,    -   (2) optionally removing unbound target-specific binding        partners,    -   (3) wherein the nucleic acid strand is a docking strand or a        primer strand and optionally if the nucleic acid is        -   (a) a docking strand, increasing the number of docking            strands associated with each target-specific binding            partner, or        -   (b) a primer strand, associating more than one docking            strand with the primer strand,    -   (4) contacting the sample with labeled imager strands having a        nucleotide sequence that is not complementary to a docking        strand or, when used, any intermediate strand,    -   (5) optionally removing unbound labeled imager strands,    -   (6) imaging the sample to detect presence, location and/or        number of bound labeled imager strands,    -   (7) extinguishing signal from the bound labeled imager strand.    -   (8) contacting the sample with labeled imager strands capable of        binding a docking strand, directly or indirectly, wherein, when        used, indirect binding is capable of occurring through an        intermediate strand,    -   (9) optionally removing unbound labeled imager strands,    -   (10) imaging the sample to detect presence, location, and/or        number of bound labeled imager strands, and    -   (11) optionally extinguishing signal from the bound labeled        imager strand.

Item 37. The method of either one of items 35 or 36, wherein the methodfurther comprises repeating steps (4)-(11).

Item 38. The method of either one of items 35-37, wherein the methodfurther comprises repeating steps to detect binding of additionalnoncomplementary imaging strands.

Item 39. The method of any one of items 35-38, wherein the labeledimager strands capable of binding a docking strand, directly orindirectly, used in the repeated steps optionally has a uniquenucleotide sequence relative to at least one other labeled imagerstrands capable of binding another docking strand, directly orindirectly.

Item 40. A composition comprising

-   -   (1) a label,    -   (2) a first nucleic acid domain, a second nucleic acid domain,        and a third nucleic acid domain, wherein each nucleic acid        domain is from 1 to 9 nucleotides long,    -   (3) a first linking moiety linking the first nucleic acid domain        and the second nucleic acid domain and    -   (4) a second linking moiety linking the second nucleic acid        domain and the third nucleic acid domain, wherein both linking        moieties are independently chosen from (a) an abasic site with        an intact phosphodiester backbone, (b) a linker cleavable by a        nucleic acid glycosylase, (c) non-natural nucleotides, or (d)        restriction site or a nicking site.

Item 41. The composition of item 40, wherein additional nucleic aciddomains are linked by additional linking moieties.

Item 42. The composition of any one of items 40-41, wherein at least onelinking moiety is an abasic site (apyrimidinic) with an intactphosphodiester backbone.

Item 43. The composition of any one of items 40-42, wherein at least onelinking moiety is susceptible to cleavage from Endonuclease VIII.

Item 44. The composition of any one of items 40-43, wherein the nucleicacid domains comprise DNA.

Item 45. The composition of any one of items 40-44, wherein the nucleicacid domains comprise RNA.

Item 46. The composition of any one of items 40-45, wherein at least onelinking moiety comprises at least one non-natural nucleotide.

Item 47. The composition of any one of items 40-46, wherein at least onelinking moiety comprises 8-oxoguanine.

Item 48. A method to test a sample for the presence of one or moretargets comprising

-   -   (1) contacting the sample with one or more target-specific        binding partners, wherein each target-specific binding partner        is linked to a nucleic acid strand, directly or indirectly and        wherein target-specific binding partners of different        specificity are linked to different nucleic acid strands,    -   (2) optionally removing unbound target-specific binding        partners,    -   (3) wherein the nucleic acid strand is a docking strand or a        primer strand and if the nucleic acid is        -   (a) a docking strand, increasing the number of docking            strands associated with each target-specific binding            partner, or        -   (b) a primer strand, associating more than one docking            strand with the primer strand,    -   (4) contacting the sample with labeled imager strands capable of        binding a docking strand, directly or indirectly, wherein the        labeled imager strands comprise the composition of any one of        items 34-41,    -   (5) optionally removing unbound labeled imager strands,    -   (6) imaging the sample to detect bound labeled imager strands,    -   (7) removing the bound labeled imager strands from the docking        strands, wherein the labeled imager strands are removed from the        docking strands by enzymatically cleaving, modifying, or        degrading the labeled imager nucleic acids,    -   (8) optionally repeating steps (1)-(7), or any subset thereof.

Item 49. The method of item 48, wherein the labeled imager nucleic acidsare removed by enzymatically cleaving the labeled imager strand.

Item 50. A method to test a sample for the presence of one or moretargets comprising

-   -   (1) treating the sample to expose one or more previously        unavailable targets,    -   (2) contacting the sample with one or more target-specific        binding partners, wherein each target-specific binding partner        is linked to a nucleic acid strand and wherein target-specific        binding partners of different specificity are linked to        different nucleic acid strands,    -   (3) optionally removing unbound target-specific binding        partners,    -   (4) wherein the nucleic acid strand is a docking strand or a        primer strand and optionally if the nucleic acid is        -   (a) a docking strand, increasing the number of docking            strands associated with each target-specific binding            partner, or        -   (b) a primer strand, associating more than one docking            strand with the primer strand,    -   (5) contacting the sample with labeled imager strands capable of        binding a docking strand, directly or indirectly,    -   (6) optionally removing unbound labeled imager strands,    -   (7) imaging the sample to detect bound labeled imager strands,    -   (8) extinguishing signal from the bound labeled imager strand,        and    -   (9) optionally repeating steps (1)-(8), each time (a) exposing a        different set of previously unavailable targets (b) using one or        more different target-specific binding partners and (c) using a        labeled imager strand having a unique nucleotide sequence        relative to at least one other labeled imager strand.

Item 51. A method to test a fixed sample mounted to a first opticallytransparent support for the presence of one or more targets comprising

-   -   (1) contacting the sample with one or more target-specific        binding partners, wherein each target-specific binding partner        is linked to a nucleic acid strand and wherein target-specific        binding partners of different specificity are linked to        different nucleic acid strands,    -   (2) optionally removing unbound target-specific binding        partners,    -   (3) wherein the nucleic acid strand is a docking strand or a        primer strand and optionally if the nucleic acid is        -   (a) a docking strand, increasing the number of docking            strands associated with each target-specific binding            partner, or        -   (b) a primer strand, associating more than one docking            strand with the primer strand,    -   (4) in an imaging chamber (such as a flow cell), contacting the        sample with labeled imager strands capable of binding a docking        strand, directly or indirectly,    -   (5) optionally removing unbound labeled imager strands,    -   (6) imaging the sample to detect presence, location, and/or        number of bound labeled imager strands,    -   (7) extinguishing signal from the bound labeled imager strand,        and    -   (8) repeating steps (4)-(6) or (4)-(7), at least once with a        labeled imager strand optionally having a unique nucleotide        sequence relative to at least one other labeled imager strands.

Item 52. The method of item 51, wherein the imaging chamber is removedafter an imaging step and before repeating steps (4)-(6) or (4)-(7).

Item 53. The method of any one of items 51-52, wherein the imagingchamber does not permit fluid flow and the imaging chamber is removedafter an imaging step and before repeating steps (4)-(6) or (4)-(7).

Item 54. The method of any one of items 51-53, where the flow cell isformed with a second optically-transparent material.

Item 55. The method of item 54, where the second optically-transparentmaterial comprises glass.

Item 56. The method of item 54, where the second optically-transparentmaterial comprises plastic.

Item 57. The method of any one of items 51-52, wherein the imagingchamber (such as a flow cell) comprises a gasket with at least one fluidinlet and/or outlet ports.

Item 58. The method of any one of items 54-56, wherein the flow cellcomprises a second optically-transparent material parallel to the firstoptically-transparent support.

Item 59. The method of any one of items 1-26, 35-39, or 48-58, whereinall fluidic exchange steps are performed using a fluidic systemcomprising electronic, and/or pneumatic, and/or hydraulic, and/orelectro-fluidic actuators and systems.

Item 60. The method of item 59, wherein the fluidic system is controlledby software.

Item 61. The method of item 59, wherein the fluidic system isautomatically controlled by software synchronizing steps (1 and/or 2and/or 3 and/or 4 and/or 5, and/or 7) with the imaging step (6), withreference to the numbering provided in item 1.

Item 62. The method of item 59, wherein the fluidic system is controlledby software synchronizing the steps (1 and/or 2 and/or 3 and/or 4 and/or5, and/or 7) with the imaging step (6) by communicating with the imagingsoftware, with reference to the numbering provided in item 1.

Item 63. The method of any one of items 59-62, wherein all fluidic stepsare performed while the sample is on the imaging device.

Item 64. The method of any one of items 59-63, wherein steps 4, 5, and 7are performed while the sample is on the imaging device, with referenceto the numbering provided in item 1.

Item 65. The method of any one of items 59-64, wherein the sample isfixed in a disposable imaging chamber (such as a flow cell).

Item 66. The method of any one of items 59-65, wherein the sample isfixed in a reusable imaging chamber (such as a flow cell).

Item 67. A kit comprising:

-   -   (1) one or more reagent(s) including but not limited to        target-specific binding partners linked to nucleic acid strands,        wherein target-specific binding partners of different        specificity are linked to different nucleic acid strands,        labeled imager strands, buffers, amplification reagents, and/or        reagents to remove bound imager strands, wherein the nucleic        acid strand is a docking strand or a primer strand and if the        nucleic acid strand is a docking strand, increasing the number        of docking strands associated with each target-specific binding        partner, or if the nucleic acid is a primer strand, associating        more than one docking strand with the primer strand,    -   (2) a fluidic system to perform all fluid exchange steps, a        software to control the fluidic system and time and/or        synchronize the fluidic steps with the imaging steps,    -   (3) a flow cell to affix on the sample of interest with at least        one optically transparent side to allow imaging of the sample.

Item 68. The kit of item 67, wherein the flow cell is a disposable flowcell.

Item 69. The method of any one of items 1-26, 35-39, or 48-66, whereinimaging the sample to detect bound labeled imager strands detects thepresence of bound labeled imager strands.

Item 70. The method of any one of items 1-26, 35-39, or 48-66, whereinimaging the sample to detect bound labeled imager strands detects thepresence, location, and/or number of bound labeled imager strands.

Item 71. The method of any one of items 70, wherein the method comprisesimaging the sample to detect and/or measure a background signal andsubtracting the background signal from the image of the sample to detectbound labeled imager strands.

Item 72. The method of item 71, wherein the background signal comprisesautofluorescence.

Item 73. The method of any one of items 71-72, wherein the backgroundcomprises residual fluorescence associated with incompletelyextinguishing signal from the bound labeled imager strands.

Item 74. The method of any one of items 71-73, wherein the backgroundsignal is measured before the image of the sample to detect boundlabeled imager strands.

Item 75. The method of any one of items 71-74, wherein the backgroundsignal is measured after the image of the sample to detect bound labeledimager strands.

Item 76. The method of any one of items 1-26, 35-39, or 48-75, whereinthe sample is a fixed sample.

Item 77. The method of any one of items 1-26, 35-39, or 48-76, whereinthe sample is a cell, cell lysate, tissue, tissue lysate, bodily fluid,and/or a whole organism.

Item 78. The method of any one of items 1-26, 35-39, or 48-77, whereinthe method is useful for identifying a biomarker.

Item 79. The method of item 78, wherein at least 96 samples are imagedand data analysis performed on those samples.

Item 80. The method of any one of items 78-79, wherein at least 15targets are tested for using corresponding target-specific bindingpartners for each target.

Item 81. The method of any one of items 1-26, 35-39, or 48-80, whereinthe imaging is performed using a light microscope, fluorescencemicroscope including widefield, confocal (line and point scanning,spinning disk), total internal reflection (TIR), stimulated emissiondepletion (STED), light-sheet illumination, structured illumination(SIM), and expansion microscopy.

Item 82. The method of any one of items 1-26, 35-39, or 48-81, whereinthe docking strand bound to a labeled imager strand, directly orindirectly, comprises at least 90% binding for 30 minutes.

Item 83. The method of any one of items 1-26, 35-39, or 48-82, whereinthe target-specific binding partner is directly linked to a dockingstrand.

Item 84. The method of any one of items 1-26, 35-39, or 48-83, whereinthe target-specific binding partner is indirectly linked to a dockingstrand through a primer strand.

Item 85. The method of any one of items 1-26, 35-39, or 48-84, whereinthe docking strand binds the imager strand directly.

Item 86. The method of any one of items 1-26, 35-39, or 48-85, whereinthe docking strand has complementarity to the imager strand.

Item 87. The method of any one of items 1-26, 35-39, or 48-86, whereinthe docking strand binds the imager strand indirectly through anintermediate strand.

Item 88. The method of any one of items 1-26, 35-39, or 48-87 or the kitof items 67-68, wherein the imager strand and/or the intermediate strandcomprises at least one U capable of cleavage by USER.

Item 89. The method of any one of items 1-26, 35-39, or 48-88 or the kitof items 66-67 and 88, wherein the imager strand and/or intermediatestrand comprises at least one abasic site.

Item 90. The method of any one of items 1-25, 34-38, or 47-89 or the kitof items 66-67 and 89, wherein the imager strand and/or the intermediatestrand comprise a hairpin.

Item 91. The method of any one of items 1-25, 34-38, or 47-90 or the kitof items 66-67 or 88-90, wherein the imager strand and/or theintermediate strand comprise a hairpin with a clamp.

Item 92. The method of any one of items 1-25, 34-38, or 47-91, whereinat least two targets are imaged using at least two labels in the sameimaging step.

Item 93. The method of any one of items 1-25, 34-38, or 47-92, whereinat least two targets are imaged using the same label in differentimaging steps.

Item 94. The method of any one of items 1-25, 34-38, or 47-93, whereinat least two targets are imaged using at least two labels, the signalextinguished, and then at least one more target is imaged using at leastone of the same labels, wherein the imaging steps may be performed ineither order.

Item 95. The method of any one of items 1-25, 34-38, or 47-93, whereinextinguishing the signal from the bound labeled imager strand comprisesremoving the nucleic acid strand from the target-specific bindingpartner.

Item 96. The method of item 95, wherein removing the nucleic acid strandcomprises enzymatically cleaving, modifying, or degrading the nucleicacid strand linked to the target specific binding partner.

Item 97. The method of item 97, wherein the nucleic acid strand isdocking strand.

Item 98. The method of item 97, wherein the nucleic acid strand is aprimer strand.

Item 99. The method of any one of items 1-25, 34-38, or 47-94, whereinif the nucleic acid strand linked to the target specific binding partneris a primer strand, extinguishing the signal from the bound labeledimager strand comprises removing the docking strand from the primerstrand.

Item 100. The method of item 99, wherein removing the docking strandcomprises enzymatically cleaving, modifying, or degrading the dockingstrand.

Item 101. The method of any one of items 1-25, 34-38, or 47-94, whereinextinguishing the signal from the bound labeled imager strand comprisesremoving the imager strand.

Item 102. The method of any one of items 1-25, 34-38, or 47-94, whereinremoving the imager strand comprises enzymatically cleaving, modifying,or degrading the imager strand.

Item 103. The method of any one of items 1-25, 34-38, or 47-94, whereinextinguishing the signal from the bound labeled imager strand comprisesremoving the label from the imager strand.

EQUIVALENTS

The foregoing written specification is sufficient to enable one skilledin the art to practice the embodiments. The foregoing description andExamples detail certain embodiments and describes the best modecontemplated by the inventors. It will be appreciated, however, that nomatter how detailed the foregoing may appear in text, the embodiment maybe practiced in many ways and should be construed in accordance with theappended claims and any equivalents thereof.

As used herein, the term about refers to a numeric value, including, forexample, whole numbers, fractions, and percentages, whether or notexplicitly indicated. The term about generally refers to a range ofnumerical values (e.g., +/−5-10% of the recited range) that one ofordinary skill in the art would consider equivalent to the recited value(e.g., having the same function or result). When terms such as at leastand about precede a list of numerical values or ranges, the terms modifyall of the values or ranges provided in the list. In some instances, theterm about may include numerical values that are rounded to the nearestsignificant figure.

1-30. (canceled)
 31. A method for detecting two or more targets,comprising: (1) contacting a sample being tested for the presence of twoor more targets with two or more target-specific binding partners,wherein each target-specific binding partner is linked to a dockingstrand and wherein target-specific binding partners of differentspecificity are linked to different docking strands; (2) optionallyremoving unbound target-specific binding partners; (3) contacting thesample with enzyme-labeled strands capable of binding a docking strand;(4) optionally removing unbound enzyme-labeled strands; (5) contactingthe sample with a substrate for the enzyme; (6) allowing an enzymaticreaction to produce an amplification product; (7) quenching theenzymatic reaction; (8) repeating steps (3)-(7); (9) imaging the sampleto detect the presence or absence of two or more targets, (10)optionally repeating at least some of steps (1)-(9).
 32. The method ofclaim 31, wherein the quenching step (7) comprises removing the boundenzyme-labeled strands.
 33. The method of claim 32, wherein the boundenzyme-labeled strands are removed by enzymatically cleaving, modifying,or degrading the enzyme-labeled strands.
 34. The method of claim 32,wherein the bound enzyme-labeled strands are removed by photochemicallycleaving the enzyme-labeled strands.
 35. The method of claim 31, furthercomprising removing or inactivating the amplification product afterimaging.
 36. The method of claim 31, wherein the enzyme-labeled strandseach comprises an enzyme capable of converting the substrate from anon-detectable state to a detectable product.
 37. The method of claim31, wherein the enzyme-labeled strands comprise horseradish peroxidase(HRP), alkaline phosphatase (AP), glucose oxidase (GO), orβ-galactosidase (β-gal).
 38. The method of claim 31, wherein thesubstrate is a chromogenic, fluorogenic, or chemiluminescent substrate.39. The method of claim 31, wherein the enzyme-labeled strands areHRP-labeled strands.
 40. The method of claim 31, wherein theenzyme-labeled strands are HRP-labeled strands and the substratecomprises a tyramide moiety linked to a fluorophore, and the enzyme iscapable of converting the tyramide moiety to an activated state capableof binding to tyrosine residues, resulting in deposition of theamplification product on or near the target.
 41. The method of claim 31,wherein the substrate comprises 3,3′-diaminobenzidine (DAB), nitro bluetetrazolium chloride (NBT), 5-bromo-4-chloro-3-indolyl phosphate (BCIP),or 5-bromo-4-chloro-3-indoyl-β-D-galactopyranoside (X-Gal).
 42. Themethod of claim 31, wherein the target-specific binding partner is anantibody or a fragment thereof.
 43. The method of claim 31, wherein thedocking strand is a nucleic acid strand.
 44. The method of claim 43,wherein the enzyme-labeled strand has a nucleic acid sequencecomplementary to a corresponding sequence of the docking strand.
 45. Themethod of claim 31, wherein at least 5 targets are tested for, using acorresponding target-specific binding partner for each target.
 46. Themethod of claim 31, wherein at least 3 targets are imaged using at least3 labels in the same imaging step.
 47. The method of claim 31, whereinat least 3 targets are imaged using at least 3 labels, the signalextinguished, and then at least one more target is imaged using at leastone of the same labels, wherein the imaging steps may be performed ineither order.
 48. A method for detecting one or more targets,comprising: (1) contacting a sample being tested for the presence of oneor more targets with one or more target-specific binding partners,wherein each target-specific binding partner is linked to a dockingstrand, and wherein target-specific binding partners of differentspecificity are linked to different docking strands, (2) optionallyremoving unbound target-specific binding partners, (3) contacting thesample with enzyme-labeled strands having a nucleotide sequence that iscomplementary to a docking strand, (4) optionally removing unboundenzyme-labeled strands, (5) contacting the sample with tyramide-bounddocking strands, wherein the docking strand is a barcode for an imagerstrand; (6) enzymatically converting the tyramide moiety into anactivated state, wherein the activated state results in a covalentlinkage of the tyramide-bound docking strand to the target site, (7)optionally quenching the enzymatic reaction, (8) optionally removing theenzyme-labeled strands, (9) optionally repeating a subset of steps 3-8;(10) contacting the sample with one or more imager strands, (11)optionally repeating at least some of steps 3-10.
 49. The method ofclaim 48, wherein the quenching step (7) comprises removing theenzyme-labeled strands.
 50. The method of claim 48, wherein the dockingstrand of the tyramide-bound docking strands comprises a nucleotidesequence complementary to the imager strand.
 51. The method of claim 48,wherein the docking strand linked to the target-specific binding partnerintroduced in step (1) is different from the docking strand of thetyramide-bound docking strands introduced in step (5).
 52. The method ofclaim 48, wherein the enzyme-labeled strands are HRP-labeled strands.53. The method of claim 48, further comprising imaging the sample todetect the presence or absence of one or more targets.
 54. The method ofclaim 53, further comprising completing at least some of steps 3-10. 55.A method for detecting two or more targets, comprising: (1) contacting asample being tested for the presence of two or more targets with two ormore target-specific binding partners, wherein each target-specificbinding partner is linked to a docking strand and whereintarget-specific binding partners of different specificity are linked todifferent docking strands; (2) optionally removing unboundtarget-specific binding partners; (3) contacting the sample withenzyme-labeled strands capable of binding a docking strand; (4)optionally removing unbound enzyme-labeled strands; (5) contacting thesample with a substrate for the enzyme; (6) allowing an enzymaticreaction to produce an amplification product; (7) quenching theenzymatic reaction; (8) imaging the sample to detect the presence orabsence of two or more targets, (9) optionally repeating at least someof steps (1)-(8).